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- PDB-9jr1: Crystal structure of CtpA from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 9jr1
TitleCrystal structure of CtpA from Helicobacter pylori
Components
  • Carboxyl-terminal protease
  • Unidentified protein
KeywordsHYDROLASE / Carboxyl-terminal processing protease / CtpA / Helicobacter pylori
Function / homology
Function and homology information


serine-type peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / signal transduction / proteolysis
Similarity search - Function
C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / PDZ domain 6 / PDZ domain / ClpP/crotonase-like domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Carboxyl-terminal protease
Similarity search - Component
Biological speciesHelicobacter pylori G27 (bacteria)
Escherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSun, K. / Au, S.W.N.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)14117622 Hong Kong
CitationJournal: To Be Published
Title: Crystal structure of CtpA from Helicobacter pylori
Authors: Sun, K. / Au, S.W.N.
History
DepositionSep 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 2.0Oct 22, 2025Group: Data collection / Polymer sequence / Structure summary
Category: entity / entity_poly ...entity / entity_poly / pdbx_validate_peptide_omega / pdbx_validate_torsion
Item: _entity.formula_weight / _entity_poly.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxyl-terminal protease
B: Carboxyl-terminal protease
C: Carboxyl-terminal protease
D: Carboxyl-terminal protease
F: Carboxyl-terminal protease
E: Carboxyl-terminal protease
S: Unidentified protein
T: Unidentified protein
H: Unidentified protein
G: Unidentified protein
K: Unidentified protein
L: Unidentified protein
I: Unidentified protein
J: Unidentified protein
N: Unidentified protein
O: Unidentified protein


Theoretical massNumber of molelcules
Total (without water)294,76116
Polymers294,76116
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29250 Å2
ΔGint-198 kcal/mol
Surface area105300 Å2
Unit cell
Length a, b, c (Å)61.696, 229.087, 116.581
Angle α, β, γ (deg.)90.00, 101.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Carboxyl-terminal protease


Mass: 46118.207 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori G27 (bacteria) / Strain: G27 / Gene: HPG27_1298 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5Z8Z7
#2: Protein/peptide
Unidentified protein


Mass: 1805.216 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 100 mM bis-tris (pH 6.5), 100 mM magnesium chloride, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→27.14 Å / Num. obs: 41187 / % possible obs: 94.6 % / Redundancy: 3.4 % / CC1/2: 0.99 / Net I/σ(I): 14.3
Reflection shellResolution: 3.4→3.52 Å / Num. unique obs: 2714 / CC1/2: 0.708

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→27.14 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 2008 4.88 %
Rwork0.1925 --
obs0.1952 41180 94.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→27.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17123 0 0 0 17123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317343
X-RAY DIFFRACTIONf_angle_d0.66923390
X-RAY DIFFRACTIONf_dihedral_angle_d5.3732364
X-RAY DIFFRACTIONf_chiral_restr0.0462763
X-RAY DIFFRACTIONf_plane_restr0.0052974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.480.3237830.2551583X-RAY DIFFRACTION54
3.48-3.580.33971360.24392429X-RAY DIFFRACTION83
3.58-3.680.31791430.22922824X-RAY DIFFRACTION96
3.68-3.80.27991500.2172887X-RAY DIFFRACTION98
3.8-3.930.30341520.20372920X-RAY DIFFRACTION99
3.93-4.090.28951490.19942958X-RAY DIFFRACTION99
4.09-4.280.20511410.18062890X-RAY DIFFRACTION99
4.28-4.50.2251530.16552959X-RAY DIFFRACTION100
4.5-4.780.21371560.15952922X-RAY DIFFRACTION99
4.78-5.150.20011480.17422968X-RAY DIFFRACTION100
5.15-5.660.24261510.19892952X-RAY DIFFRACTION100
5.66-6.470.28611450.21342958X-RAY DIFFRACTION100
6.47-8.120.26071530.20142980X-RAY DIFFRACTION100
8.12-27.140.19861480.16732942X-RAY DIFFRACTION98

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