5VFB

1.36 Angstrom Resolution Crystal Structure of Malate Synthase G from Pseudomonas aeruginosa in Complex with Glycolic Acid.

PDB DOI: https://doi.org/10.2210/pdb5VFB/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-04-07 Released: 2017-04-19
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: 1.36 Å
R-Value Free: 0.168
R-Value Work: 0.143
R-Value Observed: 0.145

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

1.36 Angstrom Resolution Crystal Structure of Malate Synthase G from Pseudomonas aeruginosa in Complex with Glycolic Acid.

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

To be published.

Macromolecule Content

Total Structure Weight: 158.72 kDa
Atom Count: 14,296
Modelled Residue Count: 1,448
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate synthase G	A, B	728	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: glcB, PA0482 EC: 2.3.3.9
UniProt
Find proteins for Q9I636 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I636 Go to UniProtKB: Q9I636
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I636
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOA Query on GOA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth B] MOL2 format, chain I [auth A] MOL2 format, chain R [auth B] mmCIF format, chain I [auth A] mmCIF format, chain R [auth B]	I [auth A], R [auth B]	GLYCOLIC ACID C₂ H₄ O₃ AEMRFAOFKBGASW-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth B] Interactions & Density Focus chain I [auth A] Focus chain R [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions 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 M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density 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 M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	K [auth B], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free: 0.168
R-Value Work: 0.143
R-Value Observed: 0.145
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m35vfb

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.385	α = 90
b = 111.712	β = 100.42
c = 96.954	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-04-19

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2017-04-19
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations