4X0O | pdb_00004x0o

Beta-ketoacyl-(acyl carrier protein) synthase III-2 (FabH2) from Vibrio cholerae soaked with Acetyl-CoA

PDB DOI: https://doi.org/10.2210/pdb4X0O/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-11-21 Released: 2014-12-03
Deposition Author(s): Hou, J., Chruszcz, M., Zheng, H., Cooper, D.R., Chordia, M.D., Zimmerman, M.D., 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: 2.20 Å
R-Value Free:
0.201 (Depositor), 0.190 (DCC)
R-Value Work:
0.173 (Depositor), 0.180 (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 1.8 of the entry. See complete history.

Literature

Structural and enzymatic studies of beta-ketoacyl-(acyl carrier protein) synthase III (FabH) from Vibrio cholerae

Hou, J., Chruszcz, M., Zheng, H., Grabowski, M., Chordia, M.D., Anderson, W.F., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 318.48 kDa
Atom Count: 22,469
Modeled Residue Count: 2,872
Deposited Residue Count: 2,896
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2	A, B, C, E, F A, B, C, E, F, G, H	362	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KLJ3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2	D	362	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KLJ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain S [auth G] SDF format, chain V [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain S [auth G] MOL2 format, chain V [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain S [auth G] mmCIF format, chain V [auth H]	I [auth A] K [auth B] N [auth D] P [auth E] Q [auth F] I [auth A], K [auth B], N [auth D], P [auth E], Q [auth F], S [auth G], V [auth H]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain S [auth G] Focus chain V [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain S [auth G] Focus chain V [auth H]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain U [auth G] MOL2 format, chain U [auth G] mmCIF format, chain U [auth G]	U [auth G]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain U [auth G] Interactions & Density Focus chain U [auth G]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain R [auth F] SDF format, chain T [auth G] SDF format, chain W [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain R [auth F] MOL2 format, chain T [auth G] MOL2 format, chain W [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain R [auth F] mmCIF format, chain T [auth G] mmCIF format, chain W [auth H]	J [auth A] L [auth B] M [auth C] O [auth D] R [auth F] J [auth A], L [auth B], M [auth C], O [auth D], R [auth F], T [auth G], W [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth F] Focus chain T [auth G] Focus chain W [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth F] Focus chain T [auth G] Focus chain W [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SCY Query on SCY	A, B, C, E, F A, B, C, E, F, G, H	L-PEPTIDE LINKING	C₅ H₉ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.201 (Depositor), 0.190 (DCC)
R-Value Work: 0.173 (Depositor), 0.180 (DCC)
R-Value Observed: 0.175 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34x0o

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.763	α = 90.06
b = 86.98	β = 89.96
c = 157.342	γ = 90.08

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2014-12-03

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	HHSN272200700058C

Revision History (Full details and data files)

Version 1.0: 2014-12-03
Type: Initial release
Version 1.1: 2015-06-03
Changes: Database references
Version 1.2: 2015-10-14
Changes: Data collection
Version 1.3: 2016-04-06
Changes: Source and taxonomy
Version 1.4: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.5: 2019-12-11
Changes: Author supporting evidence
Version 1.6: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.7: 2023-09-27
Changes: Data collection, Refinement description
Version 1.8: 2024-11-06
Changes: Structure summary

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Beta-ketoacyl-(acyl carrier protein) synthase III-2 (FabH2) from Vibrio cholerae soaked with Acetyl-CoA

Structural and enzymatic studies of beta-ketoacyl-(acyl carrier protein) synthase III (FabH) from Vibrio cholerae

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2