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- PDB-1opx: Crystal structure of the traffic ATPase (HP0525) of the Helicobac... -

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Basic information

Entry
Database: PDB / ID: 1opx
TitleCrystal structure of the traffic ATPase (HP0525) of the Helicobacter pylori type IV secretion system bound by sulfate
ComponentsvirB11 homolog
KeywordsHYDROLASE / VirB11 ATPase / bacterial type IV secretion / sulfate / HP0525 / Helicobacter pylori
Function / homology
Function and homology information


secretion by the type IV secretion system / type IV secretion system complex / nucleotide binding / ATP hydrolysis activity / metal ion binding / identical protein binding
Similarity search - Function
Type IV secretion system protein VirB11 / Beta-Lactamase - #90 / : / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich ...Type IV secretion system protein VirB11 / Beta-Lactamase - #90 / : / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsSavvides, S.N. / Yeo, H.J. / Beck, M.R. / Blaesing, F. / Lurz, R. / Lanka, E. / Buhrdorf, R. / Fischer, W. / Haas, R. / Waksman, G.
CitationJournal: Embo J. / Year: 2003
Title: VirB11 ATPases are dynamic hexameric assemblies: New insights into bacterial type IV secretion
Authors: Savvides, S.N. / Yeo, H.J. / Beck, M.R. / Blaesing, F. / Lurz, R. / Lanka, E. / Buhrdorf, R. / Fischer, W. / Haas, R. / Waksman, G.
History
DepositionMar 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: virB11 homolog
B: virB11 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4355
Polymers75,8282
Non-polymers6073
Water41423
1
A: virB11 homolog
B: virB11 homolog
hetero molecules

A: virB11 homolog
B: virB11 homolog
hetero molecules

A: virB11 homolog
B: virB11 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,30515
Polymers227,4856
Non-polymers1,8209
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area24760 Å2
ΔGint-184 kcal/mol
Surface area78830 Å2
MethodPISA, PQS
2
A: virB11 homolog
B: virB11 homolog
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)458,61130
Polymers454,97112
Non-polymers3,64018
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area52740 Å2
ΔGint-397 kcal/mol
Surface area154430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.280, 111.280, 230.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe biologically relevant hecameric assembly is generated from the dimer in the asymmetric unit by a crystallographic three fold axis

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Components

#1: Protein virB11 homolog / traffic ATPase


Mass: 37914.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: hp0525 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7BK04
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.87 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: ammonium sulfate, peg 400, tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 Mammonium sulfate1reservoir
22 %PEG4001reservoir
3100 mMTris-HCl1reservoirpH7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 8, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 18699 / Num. obs: 18699 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 11.3 Å2 / Rsym value: 0.115
Reflection shellResolution: 2.8→2.89 Å / % possible all: 66
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 80168 / Rmerge(I) obs: 0.115
Reflection shell
*PLUS
Lowest resolution: 2.9 Å / % possible obs: 94 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 8.1

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→29.63 Å / Rfactor Rfree error: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.324 728 4.7 %RANDOM
Rwork0.25 ---
all0.263 ---
obs0.252 15591 72.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.852 Å2 / ksol: 0.390312 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20.67 Å20 Å2
2--2.78 Å20 Å2
3----5.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5067 0 38 23 5128
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.562
X-RAY DIFFRACTIONc_scbond_it2.262
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 99 4.3 %
Rwork0.304 2206 -
obs--65.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION49PEG.PARAM9PEG.TOPO
X-RAY DIFFRACTION5SO4-HICUP.PARAMSO4-HICUP.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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