2YZW | pdb_00002yzw

ADP-ribosylglycohydrolase-related protein complex

• PDB DOI: https://doi.org/10.2210/pdb2YZW/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-06 Released: 2007-11-06 
• Deposition Author(s): Ebihara, A., Manzoku, M., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

ADP-ribosylglycohydrolase-related protein complex

Ebihara, A., Manzoku, M., Yokoyama, S., Kuramitsu, S.

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: 33.27 kDa 
• Atom Count: 2,383 
• Modeled Residue Count: 283 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylglycohydrolase	A	303	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SMG9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SMG9  Go to UniProtKB:  Q5SMG9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GD3	B [auth A], C [auth A]	GADOLINIUM ION Gd RJOJUSXNYCILHH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.147	α = 90
b = 73.95	β = 90
c = 78.606	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Ebihara, A., Manzoku, M., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description