7CZC | pdb_00007czc

Crystal structure of apo-FabG from Vibrio harveyi

PDB DOI: https://doi.org/10.2210/pdb7CZC/pdb

Classification: OXIDOREDUCTASE
Organism(s): Vibrio harveyi
Expression System: Escherichia coli M15
Mutation(s): No

Deposited: 2020-09-08 Released: 2021-09-08
Deposition Author(s): Singh, B.K., Kumar, A., Paul, B., Biswas, R., Das, A.K.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of apo-FabG from Vibrio harveyi

Singh, B.K., Kumar, A., Paul, B., Biswas, R., Das, A.K.

To be published.

Macromolecule Content

Total Structure Weight: 104.13 kDa
Atom Count: 7,488
Modeled Residue Count: 951
Deposited Residue Count: 964
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-ACP reductase FabG	A, B, C, D	241	Vibrio harveyi	Mutation(s): 0 Gene Names: AL538_14035, VCHENC02_3091 EC: 1.1.1.100
UniProt
Find proteins for K5VE97 (Vibrio harveyi) Explore K5VE97 Go to UniProtKB: K5VE97
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K5VE97
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.233 (Depositor), 0.230 (DCC)
R-Value Work: 0.209 (Depositor), 0.210 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.459	α = 90
b = 91.32	β = 103.22
c = 94.158	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-09-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/PR12404/BRB/10/1362/2014

Revision History (Full details and data files)

Version 1.0: 2021-09-08
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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.