2RD3 | pdb_00002rd3

Crystal structure of TenA homologue (HP1287) from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb2RD3/pdb

• Classification: HYDROLASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-21 Released: 2008-09-30 
• Deposition Author(s): Barison, N., Cendron, L., Trento, A., Angelini, A., Zanotti, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.258 (Depositor) 
• R-Value Work: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

The structural and functional characterization of HP1287 from Helicobacter pylori demonstrates it is a TenA homologue

Barison, N., Cendron, L., Trento, A., Angelini, A., Zanotti, G.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.33 kDa 
• Atom Count: 3,620 
• Modeled Residue Count: 439 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A, B [auth D]	223	Helicobacter pylori	Mutation(s): 0  Gene Names: HP1287 EC: 3.5.99.2
UniProt
Find proteins for A8KRL3 (Helicobacter pylori) Explore A8KRL3  Go to UniProtKB:  A8KRL3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.258 (Depositor) 
• R-Value Work:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.42	α = 90
b = 148.42	β = 90
c = 233.525	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-30 
Deposition Author(s): Barison, N., Cendron, L., Trento, A., Angelini, A., Zanotti, G.

Revision History  

• Version 1.0: 2008-09-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-31
  Changes: Database references
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description