5U4H | pdb_00005u4h

1.05 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Acinetobacter baumannii in Covalently Bound Complex with (2R)-2-(phosphonooxy)propanoic Acid.

PDB DOI: https://doi.org/10.2210/pdb5U4H/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-12-04 Released: 2016-12-14
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free:
0.176 (Depositor), 0.182 (DCC)
R-Value Work:
0.162 (Depositor), 0.168 (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 1.2 of the entry. See complete history.

Literature

1.05 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Acinetobacter baumannii in Covalently Bound Complex with (2R)-2-(phosphonooxy)propanoic Acid.

Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 90.65 kDa
Atom Count: 8,922
Modeled Residue Count: 840
Deposited Residue Count: 842
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 1-carboxyvinyltransferase	A, B	421	Acinetobacter baumannii	Mutation(s): 0 Gene Names: murA, A7934_11825, AA954_10900, AB895_2172, AB988_1977, ABUW_3250, ACX60_14965, APD06_13410, APD31_13720, AQ480_13100... murA, A7934_11825, AA954_10900, AB895_2172, AB988_1977, ABUW_3250, ACX60_14965, APD06_13410, APD31_13720, AQ480_13100, AQ482_08180, AZE33_03430, IOMTU433_3164, IX87_17660, LV38_01284 EC: 2.5.1.7
UniProt
Find proteins for A0A0R0VXX6 (Acinetobacter baumannii) Explore A0A0R0VXX6 Go to UniProtKB: A0A0R0VXX6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0R0VXX6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0V5 Query on 0V5 Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain K [auth A]	K [auth A], Q [auth B]	(2R)-2-(phosphonooxy)propanoic acid C₃ H₇ O₆ P CSZRNWHGZPKNKY-UWTATZPHSA-N		Interactions Focus chain K [auth A] Focus chain Q [auth B] Interactions & Density Focus chain K [auth A] Focus chain Q [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], O [auth B], P [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.176 (Depositor), 0.182 (DCC)
R-Value Work: 0.162 (Depositor), 0.168 (DCC)
R-Value Observed: 0.162 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.289	α = 90
b = 70.085	β = 110.05
c = 78.109	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-12-14

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-12-14
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.2: 2024-10-16
Changes: Structure summary