3F42 | pdb_00003f42

Crystal structure of uncharacterized protein HP0035 from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb3F42/pdb

• Classification: structural genomics, unknown function
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-31 Released: 2008-11-18 
• Deposition Author(s): Chang, C., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.220 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal structure of uncharacterized protein HP0035 from Helicobacter pylori

Chang, C., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 22.67 kDa 
• Atom Count: 1,541 
• Modeled Residue Count: 177 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein HP0035	A, B	99	Helicobacter pylori	Mutation(s): 0  Gene Names: HP_0035
UniProt
Find proteins for O24876 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O24876  Go to UniProtKB:  O24876

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth B], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.220 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.129	α = 90
b = 99.566	β = 90
c = 45.196	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-18 
Deposition Author(s): Chang, C., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-11-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Structure summary