4EVW | pdb_00004evw

Crystal Structure of the nucleoside-diphosphate-sugar pyrophosphorylase from Vibrio cholerae RC9. Northeast Structural Genomics Consortium (NESG) Target VcR193.

PDB DOI: https://doi.org/10.2210/pdb4EVW/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae RC9
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-04-26 Released: 2012-05-23
Deposition Author(s): Vorobiev, S., Neely, H., Su, M., Seetharaman, J., Mao, M., Xiao, R., Kohan, E., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.203 (Depositor), 0.199 (DCC)
R-Value Work:
0.184 (Depositor), 0.182 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the nucleoside-diphosphate-sugar pyrophosphorylase from Vibrio cholerae RC9.

Vorobiev, S., Neely, H., Su, M., Seetharaman, J., Mao, M., Xiao, R., Kohan, E., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 59.21 kDa
Atom Count: 4,383
Modeled Residue Count: 488
Deposited Residue Count: 510
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside-diphosphate-sugar pyrophosphorylase	A, B	255	Vibrio cholerae RC9	Mutation(s): 1 Gene Names: VCC_000301
UniProt
Find proteins for Q9KVB6 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVB6 Go to UniProtKB: Q9KVB6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KVB6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.203 (Depositor), 0.199 (DCC)
R-Value Work: 0.184 (Depositor), 0.182 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.303	α = 90
b = 117.003	β = 90
c = 128.561	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SnB	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-05-23

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2012-05-23
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary