6CN1

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

PDB DOI: https://doi.org/10.2210/pdb6CN1/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-03-06 Released: 2018-03-21
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Cardona-Correa, A., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.252
R-Value Work: 0.210
R-Value Observed: 0.212

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 369.52 kDa
Atom Count: 25,971
Modelled Residue Count: 3,370
Deposited Residue Count: 3,392
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 1-carboxyvinyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H	424	Pseudomonas putida KT2440	Mutation(s): 0 Gene Names: murA, PP_0964 EC: 2.5.1.7
UniProt
Find proteins for Q88P88 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88P88 Go to UniProtKB: Q88P88
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q88P88
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPU Query on EPU Download Ideal Coordinates CCD File 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 T [auth D] SDF format, chain W [auth E] SDF format, chain Z [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 T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [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 T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	DA [auth G] GA [auth H] I [auth A] M [auth B] P [auth C] DA [auth G], GA [auth H], I [auth A], M [auth B], P [auth C], T [auth D], W [auth E], Z [auth F]	URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID C₂₀ H₂₉ N₃ O₁₉ P₂ BEGZZYPUNCJHKP-DBYWSUQTSA-N		Interactions 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 T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density 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 T [auth D] Focus chain W [auth E] Focus chain Z [auth F]
0V5 Query on 0V5 Download Ideal Coordinates CCD File SDF format, chain AA [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 U [auth D] SDF format, chain X [auth E] MOL2 format, chain AA [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 U [auth D] MOL2 format, chain X [auth E] mmCIF format, chain AA [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 U [auth D] mmCIF format, chain X [auth E]	AA [auth F] EA [auth G] HA [auth H] J [auth A] N [auth B] AA [auth F], EA [auth G], HA [auth H], J [auth A], N [auth B], Q [auth C], U [auth D], X [auth E]	(2R)-2-(phosphonooxy)propanoic acid C₃ H₇ O₆ P CSZRNWHGZPKNKY-UWTATZPHSA-N		Interactions Focus chain AA [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 U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [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 U [auth D] Focus chain X [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain JA [auth H] SDF format, chain KA [auth H] SDF format, chain S [auth C] SDF format, chain L [auth A] MOL2 format, chain CA [auth F] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain L [auth A] mmCIF format, chain CA [auth F] mmCIF format, chain JA [auth H] mmCIF format, chain KA [auth H] mmCIF format, chain S [auth C] mmCIF format, chain L [auth A]	CA [auth F], JA [auth H], KA [auth H], L [auth A], S [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth F] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain L [auth A] Focus chain S [auth C] Interactions & Density Focus chain CA [auth F] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain L [auth A] Focus chain S [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain FA [auth G] SDF format, chain IA [auth H] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] SDF format, chain BA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain BA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain BA [auth F]	BA [auth F] FA [auth G] IA [auth H] K [auth A] O [auth B] BA [auth F], FA [auth G], IA [auth H], K [auth A], O [auth B], R [auth C], V [auth D], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain K [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain K [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.252
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/m36cn1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.615	α = 90
b = 148.119	β = 90
c = 164.627	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
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: 2018-03-21

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2018-03-21
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary