2DC0 | pdb_00002dc0

Crystal structure of amidase

• PDB DOI: https://doi.org/10.2210/pdb2DC0/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-12-17 Released: 2007-01-02 
• Deposition Author(s): Ohshima, T., Sakuraba, H., Ebihara, A., Kanagawa, M., Nakagawa, N., Kuroishi, C., Satoh, S., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.240 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Crystal structure of amidase

Ohshima, T., Sakuraba, H., Ebihara, A., Kanagawa, M., Nakagawa, N., Kuroishi, C., Satoh, S., Kuramitsu, S., Yokoyama, S.

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 (software)

Macromolecule Content 

• Total Structure Weight: 93.35 kDa 
• Atom Count: 6,879 
• Modeled Residue Count: 868 
• Deposited Residue Count: 868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
probable amidase	A, B	434	Thermus thermophilus	Mutation(s): 2
UniProt
Find proteins for Q5SHD3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHD3  Go to UniProtKB:  Q5SHD3

Small Molecules

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A, B	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.240 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.34	α = 90
b = 81.34	β = 90
c = 313.26	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-02 
Deposition Author(s): Ohshima, T., Sakuraba, H., Ebihara, A., Kanagawa, M., Nakagawa, N., Kuroishi, C., Satoh, S., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-01-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary