1V3Z | pdb_00001v3z

Crystal Structure of Acylphosphatase from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb1V3Z/pdb

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


• Deposited: 2003-11-07 Released: 2004-11-30 
• Deposition Author(s): Miyazono, K., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Crystal structure of acylphosphatase from hyperthermophilic archaeon Pyrococcus horikoshii OT3

Miyazono, K., Sawano, Y., Tanokura, M.

(2004) Proc Jpn Acad Ser B Phys Biol Sci 80: 439-442

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.7 kDa 
• Atom Count: 1,614 
• Modeled Residue Count: 180 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acylphosphatase	A, B	91	Pyrococcus horikoshii	Mutation(s): 0  EC: 3.6.1.7
UniProt
Find proteins for P84142 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore P84142  Go to UniProtKB:  P84142

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	C [auth A], E [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.065	α = 90
b = 86.065	β = 90
c = 75.355	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-30 
Deposition Author(s): Miyazono, K., Tanokura, M.

Revision History  

• Version 1.0: 2004-11-30
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations