3TOS | pdb_00003tos

Crystal Structure of CalS11, Calicheamicin Methyltransferase

PDB DOI: https://doi.org/10.2210/pdb3TOS/pdb

Classification: TRANSFERASE
Organism(s): Micromonospora echinospora
Mutation(s): No

Deposited: 2011-09-06 Released: 2011-10-05
Deposition Author(s): Chang, A., Aceti, D.J., Beebe, E.T., Makino, S.-I., Wrobel, R.L., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.173 (Depositor), 0.169 (DCC)
R-Value Work:
0.146 (Depositor), 0.142 (DCC)
R-Value Observed:
0.147 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of CalS11, Calicheamicin methyltransferase

Chang, A., Aceti, D.J., Beebe, E.T., Makino, S.-I., Wrobel, R.L., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N.

To be published.

Macromolecule Content

Total Structure Weight: 297.42 kDa
Atom Count: 26,923
Modeled Residue Count: 2,517
Deposited Residue Count: 2,570
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CalS11	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	257	Micromonospora echinospora	Mutation(s): 0 Gene Names: calS11
UniProt
Find proteins for Q8KNF1 (Micromonospora echinospora) Explore Q8KNF1 Go to UniProtKB: Q8KNF1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8KNF1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain GA [auth F] SDF format, chain K [auth A] SDF format, chain LA [auth G] SDF format, chain O [auth B] SDF format, chain PA [auth H] SDF format, chain S [auth C] SDF format, chain WA [auth I] SDF format, chain X [auth D] SDF format, chain YA [auth J] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain WA [auth I] MOL2 format, chain X [auth D] MOL2 format, chain YA [auth J] mmCIF format, chain CA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain PA [auth H] mmCIF format, chain S [auth C] mmCIF format, chain WA [auth I] mmCIF format, chain X [auth D] mmCIF format, chain YA [auth J]	CA [auth E] GA [auth F] K [auth A] LA [auth G] O [auth B] CA [auth E], GA [auth F], K [auth A], LA [auth G], O [auth B], PA [auth H], S [auth C], WA [auth I], X [auth D], YA [auth J]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain CA [auth E] Focus chain GA [auth F] Focus chain K [auth A] Focus chain LA [auth G] Focus chain O [auth B] Focus chain PA [auth H] Focus chain S [auth C] Focus chain WA [auth I] Focus chain X [auth D] Focus chain YA [auth J] Interactions & Density Focus chain CA [auth E] Focus chain GA [auth F] Focus chain K [auth A] Focus chain LA [auth G] Focus chain O [auth B] Focus chain PA [auth H] Focus chain S [auth C] Focus chain WA [auth I] Focus chain X [auth D] Focus chain YA [auth J]
GLU Query on GLU Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain HA [auth F] SDF format, chain L [auth A] SDF format, chain MA [auth G] SDF format, chain P [auth B] SDF format, chain QA [auth H] SDF format, chain T [auth C] SDF format, chain TA [auth I] SDF format, chain Y [auth D] SDF format, chain ZA [auth J] MOL2 format, chain DA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth I] MOL2 format, chain Y [auth D] MOL2 format, chain ZA [auth J] mmCIF format, chain DA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth I] mmCIF format, chain Y [auth D] mmCIF format, chain ZA [auth J]	DA [auth E] HA [auth F] L [auth A] MA [auth G] P [auth B] DA [auth E], HA [auth F], L [auth A], MA [auth G], P [auth B], QA [auth H], T [auth C], TA [auth I], Y [auth D], ZA [auth J]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain DA [auth E] Focus chain HA [auth F] Focus chain L [auth A] Focus chain MA [auth G] Focus chain P [auth B] Focus chain QA [auth H] Focus chain T [auth C] Focus chain TA [auth I] Focus chain Y [auth D] Focus chain ZA [auth J] Interactions & Density Focus chain DA [auth E] Focus chain HA [auth F] Focus chain L [auth A] Focus chain MA [auth G] Focus chain P [auth B] Focus chain QA [auth H] Focus chain T [auth C] Focus chain TA [auth I] Focus chain Y [auth D] Focus chain ZA [auth J]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain BB [auth J] SDF format, chain CB [auth J] SDF format, chain FA [auth E] SDF format, chain JA [auth F] SDF format, chain KA [auth F] SDF format, chain N [auth A] SDF format, chain OA [auth G] SDF format, chain R [auth B] SDF format, chain SA [auth H] SDF format, chain V [auth C] SDF format, chain VA [auth I] SDF format, chain W [auth C] SDF format, chain XA [auth I] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth J] MOL2 format, chain CB [auth J] MOL2 format, chain FA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth H] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth I] MOL2 format, chain W [auth C] MOL2 format, chain XA [auth I] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth J] mmCIF format, chain CB [auth J] mmCIF format, chain FA [auth E] mmCIF format, chain JA [auth F] mmCIF format, chain KA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth H] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth I] mmCIF format, chain W [auth C] mmCIF format, chain XA [auth I]	AA [auth D] BA [auth D] BB [auth J] CB [auth J] FA [auth E] AA [auth D], BA [auth D], BB [auth J], CB [auth J], FA [auth E], JA [auth F], KA [auth F], N [auth A], OA [auth G], R [auth B], SA [auth H], V [auth C], VA [auth I], W [auth C], XA [auth I]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain BB [auth J] Focus chain CB [auth J] Focus chain FA [auth E] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain N [auth A] Focus chain OA [auth G] Focus chain R [auth B] Focus chain SA [auth H] Focus chain V [auth C] Focus chain VA [auth I] Focus chain W [auth C] Focus chain XA [auth I] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain BB [auth J] Focus chain CB [auth J] Focus chain FA [auth E] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain N [auth A] Focus chain OA [auth G] Focus chain R [auth B] Focus chain SA [auth H] Focus chain V [auth C] Focus chain VA [auth I] Focus chain W [auth C] Focus chain XA [auth I]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AB [auth J] SDF format, chain EA [auth E] SDF format, chain IA [auth F] SDF format, chain M [auth A] SDF format, chain NA [auth G] SDF format, chain Q [auth B] SDF format, chain RA [auth H] SDF format, chain U [auth C] SDF format, chain UA [auth I] SDF format, chain Z [auth D] MOL2 format, chain AB [auth J] MOL2 format, chain EA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth H] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth I] MOL2 format, chain Z [auth D] mmCIF format, chain AB [auth J] mmCIF format, chain EA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth H] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth I] mmCIF format, chain Z [auth D]	AB [auth J] EA [auth E] IA [auth F] M [auth A] NA [auth G] AB [auth J], EA [auth E], IA [auth F], M [auth A], NA [auth G], Q [auth B], RA [auth H], U [auth C], UA [auth I], Z [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AB [auth J] Focus chain EA [auth E] Focus chain IA [auth F] Focus chain M [auth A] Focus chain NA [auth G] Focus chain Q [auth B] Focus chain RA [auth H] Focus chain U [auth C] Focus chain UA [auth I] Focus chain Z [auth D] Interactions & Density Focus chain AB [auth J] Focus chain EA [auth E] Focus chain IA [auth F] Focus chain M [auth A] Focus chain NA [auth G] Focus chain Q [auth B] Focus chain RA [auth H] Focus chain U [auth C] Focus chain UA [auth I] Focus chain Z [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.173 (Depositor), 0.169 (DCC)
R-Value Work: 0.146 (Depositor), 0.142 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.321	α = 68.69
b = 106.08	β = 69.63
c = 106.33	γ = 88.56

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-10-05

Deposition Author(s):

Center for Eukaryotic Structural Genomics (CESG)

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Revision History (Full details and data files)

Version 1.0: 2011-10-05
Type: Initial release
Version 1.1: 2012-08-08
Changes: Structure summary
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary