7P5L | pdb_00007p5l

Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 7.1 - apo form

PDB DOI: https://doi.org/10.2210/pdb7P5L/pdb

Classification: TRANSFERASE
Organism(s): Mycolicibacterium hassiacum DSM 44199
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-07-14 Released: 2023-01-18
Deposition Author(s): Silva, A., Nunes-Costa, D., Barbosa Pereira, P.J., Macedo-Ribeiro, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free:
0.164 (Depositor), 0.163 (DCC)
R-Value Work:
0.143 (Depositor), 0.143 (DCC)
R-Value Observed:
0.144 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7P5L

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

Literature

Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 7.1 - apo form

Silva, A., Nunes-Costa, D., Empadinhas, N., Barbosa Pereira, P.J., Macedo-Ribeiro, S.

To be published.

Macromolecule Content

Total Structure Weight: 70.57 kDa
Atom Count: 5,238
Modeled Residue Count: 581
Deposited Residue Count: 654
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosyl-3-phosphoglycerate synthase	A, B	327	Mycolicibacterium hassiacum DSM 44199	Mutation(s): 0 Gene Names: gpgS, C731_3243, MHAS_02845 EC: 2.4.1.266
UniProt
Find proteins for K5B7Z4 (Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849)) Explore K5B7Z4 Go to UniProtKB: K5B7Z4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K5B7Z4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLT Query on MLT Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
LMR Query on LMR Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2S)-2-hydroxybutanedioic acid C₄ H₆ O₅ BJEPYKJPYRNKOW-REOHCLBHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free: 0.164 (Depositor), 0.163 (DCC)
R-Value Work: 0.143 (Depositor), 0.143 (DCC)
R-Value Observed: 0.144 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.098	α = 90
b = 90.605	β = 90
c = 95.264	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

Nunes-Costa, D.

Barbosa Pereira, P.J.

Macedo-Ribeiro, S.

Revision History (Full details and data files)

Version 1.0: 2023-01-18
Type: Initial release
Version 1.1: 2023-03-01
Changes: Structure summary
Version 1.2: 2024-02-07
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.