5V0P | pdb_00005v0p

Crystal Structure of Beta-ketoacyl-ACP synthase III-2 (FabH2) (C113A) from Vibrio Cholerae co-crystallized with octanoyl-CoA

PDB DOI: https://doi.org/10.2210/pdb5V0P/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-02-28 Released: 2017-03-22
Deposition Author(s): Hou, J., Zheng, H., Cooper, D.R., Grabowski, M., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.207 (Depositor), 0.212 (DCC)
R-Value Work:
0.174 (Depositor), 0.186 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Beta-ketoacyl-ACP synthase III-2 (FabH2) (C113A) from Vibrio Cholerae co-crystallized with octanoyl-CoA

Hou, J., Zheng, H., Cooper, D.R., Chruszcz, M., Chordia, M.D., Grabowski, M., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 79.91 kDa
Atom Count: 5,809
Modeled Residue Count: 716
Deposited Residue Count: 724
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2	A, B	362	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 1 Gene Names: fabH2, VC_A0751 EC: 2.3.1.180
UniProt
Find proteins for Q9KLJ3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KLJ3 Go to UniProtKB: Q9KLJ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KLJ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CO8 Query on CO8 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	OCTANOYL-COENZYME A C₂₉ H₅₀ N₇ O₁₇ P₃ S KQMZYOXOBSXMII-CECATXLMSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.207 (Depositor), 0.212 (DCC)
R-Value Work: 0.174 (Depositor), 0.186 (DCC)
R-Value Observed: 0.175 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.317	α = 90
b = 61.887	β = 93.18
c = 75.734	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-03-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History (Full details and data files)

Version 1.0: 2017-03-22
Type: Initial release
Version 1.1: 2017-09-06
Changes: Author supporting evidence
Version 1.2: 2019-12-11
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description