2AP9

Crystal structure of acetylglutamate kinase from Mycobacterium tuberculosis CDC1551

PDB DOI: https://doi.org/10.2210/pdb2AP9/pdb

Classification: SIGNALING PROTEIN,TRANSFERASE
Organism(s): Mycobacterium tuberculosis CDC1551
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-08-15 Released: 2005-08-30
Deposition Author(s): Rajashankar, K.R., Kniewel, R., Lee, K., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.284
R-Value Work: 0.258
R-Value Observed: 0.258

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of acetylglutamate kinase from Mycobacterium tuberculosis CDC1551

Rajashankar, K.R., Kniewel, R., Lee, K., Lima, C.D.

To be published.

Macromolecule Content

Total Structure Weight: 191.89 kDa
Atom Count: 13,141
Modelled Residue Count: 1,762
Deposited Residue Count: 1,794
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
acetylglutamate kinase	A, B, C, D, E A, B, C, D, E, F	299	Mycobacterium tuberculosis CDC1551	Mutation(s): 7 Gene Names: argB, Rv1654, MT1692 EC: 2.7.2.8
UniProt
Find proteins for P9WQ01 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQ01 Go to UniProtKB: P9WQ01
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WQ01
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth D]	G [auth A], I [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth D]

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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.284
R-Value Work: 0.258
R-Value Observed: 0.258
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.024	α = 90
b = 122.996	β = 90
c = 194.581	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-08-30

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2005-08-30
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-04-03
Changes: Data collection, Database references, Refinement description

Prepare Data

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Deposit Data

Help and Resources

2AP9

Crystal structure of acetylglutamate kinase from Mycobacterium tuberculosis CDC1551

Crystal structure of acetylglutamate kinase from Mycobacterium tuberculosis CDC1551

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)