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- PDB-6bge: HELICOBACTER PYLORI ATPASE, HP0525, IN COMPLEX WITH 1G2 COMPOUND -

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Basic information

Entry
Database: PDB / ID: 6bge
TitleHELICOBACTER PYLORI ATPASE, HP0525, IN COMPLEX WITH 1G2 COMPOUND
ComponentsVirB11-like protein
KeywordsATP binding Protein
Function / homology
Function and homology information


secretion by the type IV secretion system / type IV secretion system complex
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
4-[(pyridin-2-yl)oxy]benzoic acid / P-type DNA transfer ATPase VirB11
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsArya, T. / Casu, B. / Baron, C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canada
CitationJournal: To Be Published
Title: CagAlpha in complex with hexamer inhibitor
Authors: Arya, T. / Casu, B. / Baron, C.
History
DepositionOct 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Dec 27, 2023Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VirB11-like protein
B: VirB11-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,43010
Polymers73,4082
Non-polymers1,0228
Water32418
1
A: VirB11-like protein
hetero molecules

A: VirB11-like protein
hetero molecules

A: VirB11-like protein
hetero molecules

B: VirB11-like protein
hetero molecules

B: VirB11-like protein
hetero molecules

B: VirB11-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,28930
Polymers220,2236
Non-polymers3,06624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area27910 Å2
ΔGint-285 kcal/mol
Surface area79700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.075, 112.075, 231.006
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 6 - 328 / Label seq-ID: 1 - 323

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein VirB11-like protein


Mass: 36703.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP0525, HPY1846_06315 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VRM0

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Non-polymers , 5 types, 26 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-DN7 / 4-[(pyridin-2-yl)oxy]benzoic acid


Mass: 215.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis Tris-HCl pH 6.5, 2.0 M ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.9→115.44 Å / Num. obs: 18083 / % possible obs: 92.4 % / Redundancy: 5.2 % / Rpim(I) all: 0.08 / Net I/σ(I): 7.4
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 1737

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G6O

1g6o


Resolution: 2.9→38.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.894 / SU B: 15.782 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.47 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2803 910 5 %RANDOM
Rwork0.22312 ---
obs0.22609 17174 91.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.33 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.9→38.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5141 0 63 18 5222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0145299
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174788
X-RAY DIFFRACTIONr_angle_refined_deg1.461.6637133
X-RAY DIFFRACTIONr_angle_other_deg0.8561.64911233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1622.975279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.56715966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5251529
X-RAY DIFFRACTIONr_chiral_restr0.0580.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025872
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02991
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0344.5562580
X-RAY DIFFRACTIONr_mcbond_other3.0324.5562580
X-RAY DIFFRACTIONr_mcangle_it4.8426.8313222
X-RAY DIFFRACTIONr_mcangle_other4.8426.8323223
X-RAY DIFFRACTIONr_scbond_it3.1594.8282719
X-RAY DIFFRACTIONr_scbond_other3.1544.8282719
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1217.1163912
X-RAY DIFFRACTIONr_long_range_B_refined7.39553.15728
X-RAY DIFFRACTIONr_long_range_B_other7.38853.1155727
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 2560 / Type: tight thermal / Rms dev position: 3.57 Å / Weight position: 0.5
LS refinement shellResolution: 2.904→2.979 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 66 -
Rwork0.316 1194 -
obs--89.11 %

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