3NZ2 | pdb_00003nz2

Crystal Structure of Hexapeptide-Repeat containing-Acetyltransferase VCA0836 Complexed with Acetyl Co Enzyme A from Vibrio cholerae O1 biovar eltor

PDB DOI: https://doi.org/10.2210/pdb3NZ2/pdb

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

Deposited: 2010-07-15 Released: 2010-08-04
Deposition Author(s): Kim, Y., Maltseva, N., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.253 (Depositor), 0.231 (DCC)
R-Value Work:
0.188 (Depositor)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Hexapeptide-Repeat containing-Acetyltransferase VCA0836 Complexed with Acetyl Co Enzyme A from Vibrio cholerae O1 biovar eltor

Kim, Y., Maltseva, N., Hasseman, J., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 271.76 kDa
Atom Count: 18,822
Modeled Residue Count: 2,198
Deposited Residue Count: 2,340
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexapeptide-repeat containing-acetyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	195	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_A0836
UniProt
Find proteins for Q9KLB0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KLB0 Go to UniProtKB: Q9KLB0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KLB0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO Query on ACO Download:Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain GA [auth H] SDF format, chain IA [auth I] SDF format, chain JA [auth I] SDF format, chain M [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth L] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain Y [auth E] SDF format, chain RA [auth L] SDF format, chain MA [auth J] MOL2 format, chain CA [auth F] MOL2 format, chain GA [auth H] MOL2 format, chain IA [auth I] MOL2 format, chain JA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth L] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain RA [auth L] MOL2 format, chain MA [auth J] mmCIF format, chain CA [auth F] mmCIF format, chain GA [auth H] mmCIF format, chain IA [auth I] mmCIF format, chain JA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth L] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain RA [auth L] mmCIF format, chain MA [auth J]	CA [auth F] GA [auth H] IA [auth I] JA [auth I] M [auth A] CA [auth F], GA [auth H], IA [auth I], JA [auth I], M [auth A], MA [auth J], P [auth A], QA [auth L], RA [auth L], T [auth C], W [auth D], Y [auth E]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain CA [auth F] Focus chain GA [auth H] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain M [auth A] Focus chain MA [auth J] Focus chain P [auth A] Focus chain QA [auth L] Focus chain RA [auth L] Focus chain T [auth C] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain GA [auth H] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain M [auth A] Focus chain MA [auth J] Focus chain P [auth A] Focus chain QA [auth L] Focus chain RA [auth L] Focus chain T [auth C] Focus chain W [auth D] Focus chain Y [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain Q [auth B] SDF format, chain SA [auth L] SDF format, chain Z [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain SA [auth L] MOL2 format, chain Z [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain SA [auth L] mmCIF format, chain Z [auth E]	DA [auth F], Q [auth B], SA [auth L], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain Q [auth B] Focus chain SA [auth L] Focus chain Z [auth E] Interactions & Density Focus chain DA [auth F] Focus chain Q [auth B] Focus chain SA [auth L] Focus chain Z [auth E]
BU1 Query on BU1 Download:Ideal Coordinates CCD File SDF format, chain FA [auth G] SDF format, chain NA [auth K] MOL2 format, chain FA [auth G] MOL2 format, chain NA [auth K] mmCIF format, chain FA [auth G] mmCIF format, chain NA [auth K]	FA [auth G], NA [auth K]	1,4-BUTANEDIOL C₄ H₁₀ O₂ WERYXYBDKMZEQL-UHFFFAOYSA-N		Interactions Focus chain FA [auth G] Focus chain NA [auth K] Interactions & Density Focus chain FA [auth G] Focus chain NA [auth K]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain EA [auth G] SDF format, chain KA [auth I] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth K] SDF format, chain PA [auth K] SDF format, chain X [auth D] SDF format, chain S [auth B] MOL2 format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain KA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth K] MOL2 format, chain PA [auth K] MOL2 format, chain X [auth D] MOL2 format, chain S [auth B] mmCIF format, chain BA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain KA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth K] mmCIF format, chain PA [auth K] mmCIF format, chain X [auth D] mmCIF format, chain S [auth B]	BA [auth F] EA [auth G] KA [auth I] N [auth A] O [auth A] BA [auth F], EA [auth G], KA [auth I], N [auth A], O [auth A], OA [auth K], PA [auth K], S [auth B], X [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain KA [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth K] Focus chain PA [auth K] Focus chain S [auth B] Focus chain X [auth D] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain KA [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth K] Focus chain PA [auth K] Focus chain S [auth B] Focus chain X [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain HA [auth H] SDF format, chain LA [auth J] SDF format, chain R [auth B] SDF format, chain U [auth C] MOL2 format, chain AA [auth E] MOL2 format, chain HA [auth H] MOL2 format, chain LA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth E] mmCIF format, chain HA [auth H] mmCIF format, chain LA [auth J] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C]	AA [auth E], HA [auth H], LA [auth J], R [auth B], U [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth E] Focus chain HA [auth H] Focus chain LA [auth J] Focus chain R [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth E] Focus chain HA [auth H] Focus chain LA [auth J] Focus chain R [auth B] Focus chain U [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain V [auth C] MOL2 format, chain V [auth C] mmCIF format, chain V [auth C]	V [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain V [auth C] Interactions & Density Focus chain V [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.253 (Depositor), 0.231 (DCC)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.191 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.316	α = 90
b = 135.801	β = 91.77
c = 120.535	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-08-04

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-22
Changes: Data collection
Version 1.4: 2024-11-20
Changes: Structure summary