5K5Y | pdb_00005k5y

Crystal structure of truncated FlgD (monoclinic form) from the human pathogen Helicobacter pylori (strain 26695)

• PDB DOI: https://doi.org/10.2210/pdb5K5Y/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-05-24 Released: 2016-12-21 
• Deposition Author(s): Kekez, I., Cendron, L., Stojanovic, M., Zanotti, G., Matkovic-Calogovic, D.
• Funding Organization(s): University of Padua

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Structure and Stability of FlgD from the Pathogenic 26695 Strain of Helicobacter pylori

Kekez, I., Cendron, L., Stojanovic, M., Zanotti, G., Matkovic-Calogovic, D.

(2016) Croat Chem Acta 

• DOI: https://doi.org/10.5562/cca2942

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 65.79 kDa 
• Atom Count: 4,641 
• Modeled Residue Count: 584 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Basal-body rod modification protein FlgD	A, B, C, D	146	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: HP_0907
UniProt
Find proteins for O25565 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25565  Go to UniProtKB:  O25565

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.51	α = 90
b = 34	β = 98.9
c = 133.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Kekez, I., Cendron, L., Stojanovic, M., Zanotti, G., Matkovic-Calogovic, D.

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Funding Organization	Location	Grant Number
University of Padua	Italy	PRIN 2010-2011 (MIUR)

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description