3DDD | pdb_00003ddd

Crystal structure of A Putative Acetyltransferase (NP_142035.1) from PYROCOCCUS HORIKOSHII at 2.25 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3DDD/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-05 Released: 2008-06-24 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.221 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.168 (Depositor) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal structure of A Putative Acetyltransferase (NP_142035.1) from PYROCOCCUS HORIKOSHII at 2.25 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 PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.7 kDa 
• Atom Count: 2,570 
• Modeled Residue Count: 281 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Acetyltransferase	A	288	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: NP_142035.1, PH0012
UniProt
Find proteins for O57768 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57768  Go to UniProtKB:  O57768

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	B [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [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: 2.25 Å
• R-Value Free:  0.221 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.168 (Depositor) 
• R-Value Observed: 0.171 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33DDD

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.673	α = 90
b = 113.673	β = 90
c = 70.756	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
autoSHARP	phasing
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-24 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-06-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, 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: 2024-10-30
  Changes: Data collection, Structure summary