6PO4 | pdb_00006po4

2.1 Angstrom Resolution Crystal Structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (mtnN) from Haemophilus influenzae PittII.

PDB DOI: https://doi.org/10.2210/pdb6PO4/pdb

Classification: HYDROLASE
Organism(s): Haemophilus influenzae PittII
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-07-03 Released: 2019-07-17
Deposition Author(s): Minasov, G., Shuvalova, L., Cardona-Correa, A., Dubrovska, I., Grimshaw, S., Kwon, K., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.191 (Depositor), 0.200 (DCC)
R-Value Work:
0.160 (Depositor), 0.170 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

2.1 Angstrom Resolution Crystal Structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (mtnN) from Haemophilus influenzae PittII.

Minasov, G., Shuvalova, L., Cardona-Correa, A., Dubrovska, I., Grimshaw, S., Kwon, K., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 149.56 kDa
Atom Count: 11,189
Modeled Residue Count: 1,394
Deposited Residue Count: 1,404
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase	A, B, C, D, E A, B, C, D, E, F	234	Haemophilus influenzae PittII	Mutation(s): 0 Gene Names: mtnN, CGSHiII_00894 EC: 3.2.2.9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HCS (Subject of Investigation/LOI) Query on HCS Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain T [auth E] SDF format, chain W [auth F] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F]	G [auth A] K [auth B] N [auth C] O [auth C] T [auth E] G [auth A], K [auth B], N [auth C], O [auth C], T [auth E], W [auth F]	2-AMINO-4-MERCAPTO-BUTYRIC ACID C₄ H₉ N O₂ S FFFHZYDWPBMWHY-VKHMYHEASA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain T [auth E] Focus chain W [auth F]
ADE (Subject of Investigation/LOI) Query on ADE Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain V [auth F] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain V [auth F]	H [auth A] J [auth B] M [auth C] Q [auth D] S [auth E] H [auth A], J [auth B], M [auth C], Q [auth D], S [auth E], V [auth F]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain V [auth F]
BO3 Query on BO3 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain X [auth F] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain X [auth F]	I [auth A] L [auth B] P [auth C] R [auth D] U [auth E] I [auth A], L [auth B], P [auth C], R [auth D], U [auth E], X [auth F]	BORIC ACID B H₃ O₃ KGBXLFKZBHKPEV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.191 (Depositor), 0.200 (DCC)
R-Value Work: 0.160 (Depositor), 0.170 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.536	α = 90
b = 214.743	β = 90
c = 146.904	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MoRDa	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-07-17

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2019-07-17
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-04-03
Changes: Structure summary