4EG2 | pdb_00004eg2

2.2 Angstrom Crystal Structure of Cytidine deaminase from Vibrio cholerae in Complex with Zinc and Uridine

PDB DOI: https://doi.org/10.2210/pdb4EG2/pdb

Classification: HYDROLASE
Organism(s): Vibrio cholerae
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2012-03-30 Released: 2012-05-02
Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Wang, Y., Grimshaw, S., Papazisi, L., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.210 (Depositor), 0.220 (DCC)
R-Value Work:
0.159 (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 1.4 of the entry. See complete history.

Literature

2.2 Angstrom Crystal Structure of Cytidine deaminase from Vibrio cholerae in Complex with Zinc and Uridine.

Minasov, G., Wawrzak, Z., Skarina, T., Wang, Y., Grimshaw, S., Papazisi, L., Savchenko, A., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 265.18 kDa
Atom Count: 19,771
Modeled Residue Count: 2,374
Deposited Residue Count: 2,384
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytidine deaminase	A, B, C, D, E A, B, C, D, E, F, G, H	298	Vibrio cholerae	Mutation(s): 0 Gene Names: cdd, VC_1231 EC: 3.5.4.5
UniProt
Find proteins for Q9KSM5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KSM5 Go to UniProtKB: Q9KSM5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KSM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URI Query on URI Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain W [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain W [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain W [auth E]	BA [auth F] EA [auth G] HA [auth H] J [auth A] N [auth B] BA [auth F], EA [auth G], HA [auth H], J [auth A], N [auth B], Q [auth C], S [auth D], W [auth E]	URIDINE C₉ H₁₂ N₂ O₆ DRTQHJPVMGBUCF-XVFCMESISA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain W [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain W [auth E]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain DA [auth G] SDF format, chain GA [auth H] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain V [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain V [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain V [auth E]	AA [auth F] DA [auth G] GA [auth H] I [auth A] M [auth B] AA [auth F], DA [auth G], GA [auth H], I [auth A], M [auth B], P [auth C], R [auth D], V [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain V [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain V [auth E]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain FA [auth G] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E]	CA [auth F] FA [auth G] K [auth A] O [auth B] T [auth D] CA [auth F], FA [auth G], K [auth A], O [auth B], T [auth D], U [auth D], X [auth E], Y [auth E], Z [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth F] Focus chain FA [auth G] Focus chain K [auth A] Focus chain O [auth B] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain FA [auth G] Focus chain K [auth A] Focus chain O [auth B] Focus chain T [auth D] Focus chain U [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]

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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.210 (Depositor), 0.220 (DCC)
R-Value Work: 0.159 (Depositor), 0.170 (DCC)
R-Value Observed: 0.162 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34eg2

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.81	α = 90
b = 163.73	β = 97.7
c = 111.95	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-05-02

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-05-02
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection
Version 1.4: 2024-10-09
Changes: Structure summary