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- PDB-1s2x: Crystal structure of Cag-Z from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 1s2x
TitleCrystal structure of Cag-Z from Helicobacter pylori
ComponentsCag-Z
KeywordsUNKNOWN FUNCTION / Cag-Z / Helicobacter pylori / cag pathogenicity island / type IV secretion system
Function / homologyCAG pathogenicity island protein, CagZ / Cag pathogenicity island protein, CagZ / Cag-Z superfamily / CagZ / Delta-Endotoxin; domain 1 / Up-down Bundle / Mainly Alpha / ISOPROPYL ALCOHOL / Cag-Z
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsCendron, L. / Seydel, A. / Angelini, A. / Battistutta, R. / Zanotti, G.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of CagZ, a protein from the Helicobacter pylori pathogenicity island that encodes for a type IV secretion system
Authors: Cendron, L. / Seydel, A. / Angelini, A. / Battistutta, R. / Zanotti, G.
History
DepositionJan 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cag-Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9982
Polymers23,9381
Non-polymers601
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.550, 44.650, 159.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cag-Z


Mass: 23938.371 Da / Num. of mol.: 1 / Mutation: M1D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: cagZ / Plasmid: pGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9JMX9
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000, isopropanol, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9202 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 10, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.9→45 Å / Num. all: 18377 / Num. obs: 18377 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 5
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2406 / % possible all: 92.5

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→8 Å / Num. parameters: 6267 / Num. restraintsaints: 5971
Isotropic thermal model: Isotropic, Anisotropic only for 4 Se atoms
Cross valid method: FREE R / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1381 -RANDOM
Rwork0.238 ---
all0.245 17961 --
obs0.229 14273 88.9 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1556
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 0 95 1558
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0217
X-RAY DIFFRACTIONs_zero_chiral_vol0.026
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.03
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.085
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.9-20.353X-RAY DIFFRACTION213312.86
2-2.20.278X-RAY DIFFRACTION356821.52
2.2-2.50.231X-RAY DIFFRACTION346320.89
2.5-30.215X-RAY DIFFRACTION314718.98
3-40.218X-RAY DIFFRACTION256715.48
4-80.257X-RAY DIFFRACTION169710.23

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