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- PDB-3cwy: Structure of CagD from H. pylori pathogenicity island crystallize... -

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Basic information

Entry
Database: PDB / ID: 3cwy
TitleStructure of CagD from H. pylori pathogenicity island crystallized in the presence of Cu(II) ions
Componentsprotein CagD
KeywordsUNKNOWN FUNCTION / CagD / cag-pathogenicity island / Type IV secretion system / T4SS
Function / homology
Function and homology information


Pathogenicity 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 / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / CagD
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 ...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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 2024Group: Structure summary / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8412
Polymers20,7771
Non-polymers641
Water19811
1
A: protein CagD
hetero molecules

A: protein CagD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6824
Polymers41,5552
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area2190 Å2
ΔGint-32 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.030, 65.030, 156.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein protein CagD / HP0525 / Cag24


Mass: 20777.463 Da / Num. of mol.: 1 / 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: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 0.2 M MgCl2, 0.1 M Hepes pH 7, 20% PEG 6000, CuCl2 0.02M , VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97621 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 31, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97621 Å / Relative weight: 1
ReflectionResolution: 2.75→78.09 Å / Num. all: 5757 / Num. obs: 5757 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.5
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 1.7 / Num. unique all: 796 / % possible all: 99

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CWX

3cwx


Resolution: 2.75→56.34 Å / Rfactor Rfree error: 0.019 / Data cutoff high absF: 1913839.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.307 252 4.5 %RANDOM
Rwork0.261 ---
all0.262 0 --
obs0.262 5322 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT MODEL / Bsol: 102.977 Å2 / ksol: 0.708042 e/Å3
Displacement parametersBiso mean: 56.67 Å2
Baniso -1Baniso -2Baniso -3
1-4.09 Å22.05 Å20 Å2
2--4.09 Å20 Å2
3----6.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.75→56.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 1 11 1087
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.59
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.4782
X-RAY DIFFRACTIONc_mcangle_it2.5313
X-RAY DIFFRACTIONc_scbond_it1.2552
X-RAY DIFFRACTIONc_scangle_it1.8373
LS refinement shellResolution: 2.75→2.82 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 18 6 %
Rwork0.292 391 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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