3PZC

Crystal structure of class II aaRS homologue (Bll0957) complexed with Coenzyme A

PDB DOI: https://doi.org/10.2210/pdb3PZC/pdb

Classification: LIGASE
Organism(s): Bradyrhizobium japonicum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-12-14 Released: 2011-10-19
Deposition Author(s): Weygand-Durasevic, I., Luic, M., Mocibob, M., Ivic, N., Subasic, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.223
R-Value Work: 0.167
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Substrate Recognition by Novel Family of Amino Acid:[Carrier Protein] Ligases

Mocibob, M., Ivic, N., Subasic, D., Luic, M., Weygand-Durasevic, I.

(2011) Croat Chem Acta 84: 149-157

DOI: https://doi.org/10.5562/cca1818

Macromolecule Content

Total Structure Weight: 77.98 kDa
Atom Count: 4,996
Modelled Residue Count: 572
Deposited Residue Count: 692
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid--[acyl-carrier-protein] ligase 1	A, B	346	Bradyrhizobium japonicum	Mutation(s): 0 Gene Names: bll0957 EC: 6.2.1
UniProt
Find proteins for Q89VT8 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore Q89VT8 Go to UniProtKB: Q89VT8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q89VT8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
GAP Query on GAP Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	GLYCYL-ADENOSINE-5'-PHOSPHATE C₁₂ H₁₇ N₆ O₈ P HROXHMRQKGGIFT-JJNLEZRASA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B]	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	I [auth B], J [auth B], K [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.223
R-Value Work: 0.167
R-Value Observed: 0.170
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.194	α = 90
b = 101.791	β = 90
c = 50.623	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
CrysalisPro	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-10-19

Deposition Author(s):

Weygand-Durasevic, I.

Revision History (Full details and data files)

Version 1.0: 2011-10-19
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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Help and Resources

3PZC

Crystal structure of class II aaRS homologue (Bll0957) complexed with Coenzyme A

Substrate Recognition by Novel Family of Amino Acid:[Carrier Protein] Ligases

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)