3TNV | pdb_00003tnv

Acylphosphatase with thermophilic surface and mesophilic core

• PDB DOI: https://doi.org/10.2210/pdb3TNV/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-09-02 Released: 2012-09-05 
• Deposition Author(s): Yu, T.H., Chan, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.167 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Protein surface is a preferred site for thermostability engineering

Yu, T.H., Wong, K.B.

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)

Macromolecule Content 

• Total Structure Weight: 10.47 kDa 
• Atom Count: 877 
• Modeled Residue Count: 90 
• Deposited Residue Count: 91 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acylphosphatase	A	91	Pyrococcus horikoshii OT3	Mutation(s): 8  Gene Names: acyP, PH0305.1 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.167 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.087	α = 90
b = 44.438	β = 100.99
c = 30.813	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Yu, T.H., Chan, C.H.

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description