2Q0Y | pdb_00002q0y

Crystal structure of GCN5-related N-acetyltransferase (YP_295895.1) from Ralstonia eutropha JMP134 at 1.80 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2Q0Y/pdb

• Classification: TRANSFERASE
• Organism(s): Cupriavidus pinatubonensis JMP134
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-05-22 Released: 2007-06-05 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.165 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Literature

Crystal structure of GCN5-related N-acetyltransferase (YP_295895.1) from Ralstonia eutropha JMP134 at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 17.92 kDa 
• Atom Count: 1,447 
• Modeled Residue Count: 153 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN5-related N-acetyltransferase	A	153	Cupriavidus pinatubonensis JMP134	Mutation(s): 9  Gene Names: YP_295895.1, Reut_A1686
UniProt
Find proteins for Q470Y2 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q470Y2  Go to UniProtKB:  Q470Y2

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	G [auth A], H [auth A], I [auth A], J [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL	E [auth A]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.165 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32Q0Y

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.52	α = 90
b = 102.52	β = 90
c = 39.68	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-05 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-06-05
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.6: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.7: 2024-11-20
  Changes: Data collection, Structure summary