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
View more details

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]	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 E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D]	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 F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D]	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

Prepare Data

Validate Data

Deposit Data

Help and Resources

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.

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.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)