9JR1 | pdb_00009jr1

Crystal structure of CtpA from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb9JR1/pdb
• NAKB: 9JR1

• Classification: HYDROLASE
• Organism(s): Helicobacter pylori G27, Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-29 Released: 2025-10-01 
• Deposition Author(s): Sun, K., Au, S.W.N.
• Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of CtpA from Helicobacter pylori

Sun, K., Au, S.W.N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 14-mer - A6B4C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 14-mer - A4B2C1D1E1F1G1H1I1J1 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 294.76 kDa 
• Atom Count: 17,123 
• Modeled Residue Count: 2,255 
• Deposited Residue Count: 2,706 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxyl-terminal protease	A, B, C, D, E [auth F], F [auth E]	416	Helicobacter pylori G27	Mutation(s): 0  Gene Names: HPG27_1298
UniProt
Find proteins for B5Z8Z7 (Helicobacter pylori (strain G27)) Explore B5Z8Z7  Go to UniProtKB:  B5Z8Z7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Unidentified protein	G [auth S], H [auth T], I [auth H], J [auth G], K, L, M [auth I], N [auth J], O [auth N], P [auth O]	21	Escherichia coli BL21(DE3)	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.696	α = 90
b = 229.087	β = 101.26
c = 116.581	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Sun, K., Au, S.W.N.

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Funding Organization	Location	Grant Number
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	14117622

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release
  
• Version 2.0: 2025-10-22
  Changes: Data collection, Polymer sequence, Structure summary