5WI5

2.0 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium.

PDB DOI: https://doi.org/10.2210/pdb5WI5/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-07-18 Released: 2017-08-02
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.266
R-Value Work: 0.222
R-Value Observed: 0.225

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

2.0 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Streptococcus pneumoniae in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium.

Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 188.26 kDa
Atom Count: 13,657
Modelled Residue Count: 1,687
Deposited Residue Count: 1,720
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1	A, B, C, D	430	Streptococcus pneumoniae TIGR4	Mutation(s): 0 Gene Names: murA1, murA, SP_1966 EC: 2.5.1.7
UniProt
Find proteins for Q97NQ4 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q97NQ4 Go to UniProtKB: Q97NQ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q97NQ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPU (Subject of Investigation/LOI) Query on EPU Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A], J [auth B], M [auth C], P [auth D]	URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID C₂₀ H₂₉ N₃ O₁₉ P₂ BEGZZYPUNCJHKP-DBYWSUQTSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
0V5 (Subject of Investigation/LOI) Query on 0V5 Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B], K [auth C], N [auth D]	(2R)-2-(phosphonooxy)propanoic acid C₃ H₇ O₆ P CSZRNWHGZPKNKY-UWTATZPHSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain F [auth A]	F [auth A], I [auth B], L [auth C], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.266
R-Value Work: 0.222
R-Value Observed: 0.225
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m35wi5

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.243	α = 90
b = 80.13	β = 95.76
c = 126.511	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-08-02

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2017-08-02
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description