4XFJ

Crystal structure of Argininosuccinate synthase from Mycobacterium thermoresistibile in complex with AMPPNP and Arginine

PDB DOI: https://doi.org/10.2210/pdb4XFJ/pdb

Classification: LIGASE
Organism(s): Mycolicibacterium thermoresistibile ATCC 19527
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-12-27 Released: 2015-01-14
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.182
R-Value Work: 0.136
R-Value Observed: 0.138

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 Argininosuccinate synthase from Mycobacterium thermoresistibile in complex with AMPPNP and Arginine

Abendroth, J., Dranow, D.M., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 92.16 kDa
Atom Count: 7,173
Modelled Residue Count: 792
Deposited Residue Count: 816
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Argininosuccinate synthase	A, B	408	Mycolicibacterium thermoresistibile ATCC 19527	Mutation(s): 0 Gene Names: argG, KEK_01915 EC: 6.3.4.5
UniProt
Find proteins for G7CBN9 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)) Explore G7CBN9 Go to UniProtKB: G7CBN9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G7CBN9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B]	C [auth A], K [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
ARG Query on ARG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B]	E [auth A], M [auth B]	ARGININE C₆ H₁₅ N₄ O₂ ODKSFYDXXFIFQN-BYPYZUCNSA-O		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	F [auth A] G [auth A] I [auth A] J [auth B] N [auth B] F [auth A], G [auth A], I [auth A], J [auth B], N [auth B], O [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain N [auth B] Focus chain O [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B]	D [auth A], H [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.182
R-Value Work: 0.136
R-Value Observed: 0.138
Space Group: P 2₁ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M34XFJ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.83	α = 90
b = 143.41	β = 90
c = 58.03	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
Coot	model building
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-01-14

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-01-14
Type: Initial release
Version 1.1: 2015-01-21
Changes: Data collection
Version 1.2: 2017-11-22
Changes: Derived calculations, Refinement description, Source and taxonomy, Structure summary
Version 1.3: 2018-03-07
Changes: Data collection
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4XFJ

Crystal structure of Argininosuccinate synthase from Mycobacterium thermoresistibile in complex with AMPPNP and Arginine

Crystal structure of Argininosuccinate synthase from Mycobacterium thermoresistibile in complex with AMPPNP and Arginine

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)