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- PDB-3cwx: Crystal structure of cagd from helicobacter pylori pathogenicity ... -

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Basic information

Entry
Database: PDB / ID: 3cwx
TitleCrystal structure of cagd from helicobacter pylori pathogenicity island
Componentsprotein CagD
KeywordsUNKNOWN FUNCTION / CagD / cag-pathogenicity island / Type IV secretion system / T4SS
Function / homologyPathogenicity island component CagD / Pathogenicity island component CagD / Pathogenicity island component CagD superfamily / Pathogenicity island component CagD / Inhibitor of vertebrate lysozyme, Ivy / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / CagD
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsCendron, L. / Zanotti, G. / Angelini, A. / Barison, N. / Couturier, M. / Stein, M.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: The Helicobacter pylori CagD (HP0545, Cag24) protein is essential for CagA translocation and maximal induction of interleukin-8 secretion.
Authors: Cendron, L. / Couturier, M. / Angelini, A. / Barison, N. / Stein, M. / Zanotti, G.
#1: Journal: 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.
#2: Journal: Proteins: Struct.,Funct.,Genet. / Year: 2007
Title: The crystal structure of CagS from the Helicobacter pylori pathogenicity island
Authors: Cendron, L. / Tasca, E. / Seraglio, T. / Seydel, A. / Angelini, A. / Battistutta, R. / Montecucco, C. / Zanotti, G.
History
DepositionApr 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.4Oct 30, 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: protein CagD
B: protein CagD
C: protein CagD


Theoretical massNumber of molelcules
Total (without water)62,3323
Polymers62,3323
Non-polymers00
Water2,846158
1
A: protein CagD
B: protein CagD


Theoretical massNumber of molelcules
Total (without water)41,5552
Polymers41,5552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-8 kcal/mol
Surface area14140 Å2
MethodPISA
2
C: protein CagD

C: protein CagD


Theoretical massNumber of molelcules
Total (without water)41,5552
Polymers41,5552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area1730 Å2
ΔGint-11 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.181, 117.956, 65.157
Angle α, β, γ (deg.)90.00, 110.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein protein CagD / HP0525 / Cag24


Mass: 20777.463 Da / Num. of mol.: 3 / Fragment: CagD / Mutation: V79M, V140M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: CCUG 17874 / Gene: cagD / Plasmid: pET28b-cagD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P94837
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 0.2 M MgGl2, 0.1M Hepes, 20% PEG 6000, pH 7, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97942, 0.97420, 0.97814
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.97421
30.978141
ReflectionResolution: 2.2→62.26 Å / Num. all: 28577 / Num. obs: 28577 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 4.1 / Num. unique all: 4107 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→62.26 Å / Num. parameters: 13079 / Num. restraintsaints: 12726 / Cross valid method: FREE R / σ(F): 0 / 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
Rfree0.288 2783 10 %RANDOM
all0.242 27833 --
obs0.242 27833 99.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3361
Refinement stepCycle: LAST / Resolution: 2.3→62.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3105 0 0 158 3263
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0232
X-RAY DIFFRACTIONs_zero_chiral_vol0.024
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.032
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.097
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 2.3→2.4 Å
RfactorNum. reflection% reflection
Rfree0.303 446 -
Rwork0.238 --
obs-4287 9.8 %

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