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- PDB-1nly: Crystal structure of the traffic ATPase of the Helicobacter pylor... -

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Basic information

Entry
Database: PDB / ID: 1nly
TitleCrystal structure of the traffic ATPase of the Helicobacter pylori type IV secretion system in complex with ATPgammaS
ComponentsvirB11 homolog
KeywordsHYDROLASE / VIRB11 ATPase / bacterial type IV secretion / ATPgammaS / HP0525 / Helicobacter pylori
Function / homology
Function and homology information


secretion by the type IV secretion system / type IV secretion system complex / nucleotide 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Cag alpha
Similarity search - Component
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
DepositionJan 8, 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: Source and taxonomy / Version format compliance
Revision 1.3Mar 7, 2012Group: Non-polymer description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,4107
Polymers75,8282
Non-polymers1,5815
Water75742
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)232,23021
Polymers227,4856
Non-polymers4,74415
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
Unit cell
Length a, b, c (Å)110.820, 110.820, 230.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe biologically relevant hexameric assembly is generated from the dimer in the asymmetric unit by a crystallographic three fold axis

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein virB11 homolog


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

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Non-polymers , 5 types, 47 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.56 %
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 298.0K
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
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. obs: 21264 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 27.6 Å2 / Rsym value: 0.095
Reflection shellHighest resolution: 2.9 Å / Rsym value: 0.378 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 21297 / % possible obs: 99.1 % / Num. measured all: 110109 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→19.99 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.304 773 4.8 %RANDOM
Rwork0.243 ---
all0.264 21297 --
obs-16131 75.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.3828 Å2 / ksol: 0.358222 e/Å3
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å2-1.65 Å20 Å2
2--1.93 Å20 Å2
3----3.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5103 0 96 42 5241
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.81.5
X-RAY DIFFRACTIONc_mcangle_it3.012
X-RAY DIFFRACTIONc_scbond_it2.752
X-RAY DIFFRACTIONc_scangle_it4.142.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 94 4.6 %
Rwork0.278 1955 -
obs--58.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ATPGS+ADP.PARAMATPGS+ADP.TOPO
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION49PEG.PARAM9PEG.TOPO
X-RAY DIFFRACTION5ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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