3GYA | pdb_00003gya

Crystal structure of putative acetyltransferase (YP_001815201.1) from EXIGUOBACTERIUM SP. 255-15 at 1.62 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3GYA/pdb

• Classification: TRANSFERASE
• Organism(s): Exiguobacterium artemiae 255-15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-03 Released: 2009-04-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.204 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Crystal structure of putative acetyltransferase (YP_001815201.1) from EXIGUOBACTERIUM SP. 255-15 at 1.62 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.32 kDa 
• Atom Count: 1,449 
• Modeled Residue Count: 147 
• Deposited Residue Count: 150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GCN5-related N-acetyltransferase	A	150	Exiguobacterium artemiae 255-15	Mutation(s): 0  Gene Names: Exig_2736, YP_001815201.1
UniProt
Find proteins for B1YEL6 (Exiguobacterium sibiricum (strain DSM 17290 / CCUG 55495 / CIP 109462 / JCM 13490 / 255-15)) Explore B1YEL6  Go to UniProtKB:  B1YEL6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	B [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.62 Å
• R-Value Free:  0.204 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33GYA

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.793	α = 90
b = 66.249	β = 90
c = 87.769	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary