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- PDB-5lp2: Adhesin domain of the type 1 HopQ of Helicobacter pylori strain G27 -

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Basic information

Entry
Database: PDB / ID: 5lp2
TitleAdhesin domain of the type 1 HopQ of Helicobacter pylori strain G27
ComponentsHopQ
KeywordsCELL ADHESION / adhesin / Helicobacter outer membrane protein / ectodomain / CEACAM
Function / homologySabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Outer membrane protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMoonens, K. / Kruse, T. / Gerhard, M. / Remaut, H.
Funding support Belgium, 1items
OrganizationGrant numberCountry
FWOG.0902.09 Belgium
CitationJournal: Nat Microbiol / Year: 2016
Title: Helicobacter pylori adhesin HopQ engages in a virulence-enhancing interaction with human CEACAMs.
Authors: Javaheri, A. / Kruse, T. / Moonens, K. / Mejias-Luque, R. / Debraekeleer, A. / Asche, C.I. / Tegtmeyer, N. / Kalali, B. / Bach, N.C. / Sieber, S.A. / Hill, D.J. / Koniger, V. / Hauck, C.R. / ...Authors: Javaheri, A. / Kruse, T. / Moonens, K. / Mejias-Luque, R. / Debraekeleer, A. / Asche, C.I. / Tegtmeyer, N. / Kalali, B. / Bach, N.C. / Sieber, S.A. / Hill, D.J. / Koniger, V. / Hauck, C.R. / Moskalenko, R. / Haas, R. / Busch, D.H. / Klaile, E. / Slevogt, H. / Schmidt, A. / Backert, S. / Remaut, H. / Singer, B.B. / Gerhard, M.
History
DepositionAug 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: HopQ
A: HopQ
C: HopQ
D: HopQ


Theoretical massNumber of molelcules
Total (without water)186,5214
Polymers186,5214
Non-polymers00
Water63135
1
B: HopQ


Theoretical massNumber of molelcules
Total (without water)46,6301
Polymers46,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: HopQ


Theoretical massNumber of molelcules
Total (without water)46,6301
Polymers46,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HopQ


Theoretical massNumber of molelcules
Total (without water)46,6301
Polymers46,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HopQ


Theoretical massNumber of molelcules
Total (without water)46,6301
Polymers46,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.700, 57.700, 285.600
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13B
23D
14A
24C
15A
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010B28 - 431
2010A28 - 431
1020B28 - 431
2020C28 - 431
1030B - G28 - 431
2030D28 - 431
1040A28 - 431
2040C28 - 431
1050A28 - 431
2050D28 - 431
1060C28 - 431
2060D28 - 431

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
HopQ


Mass: 46630.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: adhesin domain comprising residues 16 to 442, a C-terminal histidine tag is present
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: hopQ, HPG27_1120 / Plasmid: pPRkana-1 / Details (production host): derivative of pPR-IBA 1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5Z8H1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.12M alcohols (0.02M 1,6-Hexanediol; 0.02M 1-Butanol; 0.02M 1,2-Propanediol; 0.02M 2-Propanol; 0.02M 1,4-Butanediol; 0.02M 1,3-Propanediol), 0.1 M Tris (base)/BICINE pH 8.5, 20% v/v PEG ...Details: 0.12M alcohols (0.02M 1,6-Hexanediol; 0.02M 1-Butanol; 0.02M 1,2-Propanediol; 0.02M 2-Propanol; 0.02M 1,4-Butanediol; 0.02M 1,3-Propanediol), 0.1 M Tris (base)/BICINE pH 8.5, 20% v/v PEG 500* MME; 10 % w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→49.4 Å / Num. obs: 55541 / % possible obs: 99.7 % / Redundancy: 4.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.147 / Net I/σ(I): 7.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 0.9 / CC1/2: 0.576 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F7K

5f7k


Resolution: 2.6→49.4 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 31.911 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 0.535 / ESU R Free: 0.278 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23617 2924 5 %RANDOM
Rwork0.20768 ---
obs0.20912 55541 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.023 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å2-0 Å2-0.77 Å2
2--0.81 Å2-0 Å2
3----1.82 Å2
Refinement stepCycle: 1 / Resolution: 2.6→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10952 0 0 35 10987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211092
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210504
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.94415020
X-RAY DIFFRACTIONr_angle_other_deg0.912324164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.48251420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.6627.576528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.983151960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2481516
X-RAY DIFFRACTIONr_chiral_restr0.0920.21736
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213052
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022476
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_it3.294.0345740
X-RAY DIFFRACTIONr_mcbond_other3.2884.0345739
X-RAY DIFFRACTIONr_mcangle_it5.1986.0337140
X-RAY DIFFRACTIONr_mcangle_other5.1986.0347141
X-RAY DIFFRACTIONr_scbond_it3.9314.4275352
X-RAY DIFFRACTIONr_scbond_other3.9314.4275353
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3976.4487881
X-RAY DIFFRACTIONr_long_range_B_refined8.50131.46912244
X-RAY DIFFRACTIONr_long_range_B_other8.531.47112245
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11B21717
12A21717
21B21723
22C21723
31B21706
32D21706
41A21723
42C21723
51A21706
52D21706
61C21713
62D21713
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.492 210 -
Rwork0.456 3991 -
obs--99.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3354-0.10480.58430.524-0.77351.88380.09490.00590.0256-0.0478-0.13740.01950.10710.01870.04250.33380.1331-0.02730.3368-0.03560.0108-0.757639.149347.5188
20.60170.1593-0.84620.3979-0.69951.9727-0.12090.04230.0441-0.01720.1149-0.00820.0324-0.11750.0060.3863-0.1309-0.05370.29110.00490.0173-9.177619.9315118.9028
30.5529-0.14470.77110.3892-0.6721.941-0.1348-0.0495-0.03190.02070.1052-0.0155-0.0425-0.12270.02960.38660.1310.00770.28490.00240.012619.844418.586223.8795
40.40950.1535-0.64580.5777-0.80591.96910.1082-0.0251-0.00810.0425-0.13560.0487-0.11930.02720.02740.333-0.1339-0.01440.338-0.0350.021528.0014-0.63195.2679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B28 - 431
2X-RAY DIFFRACTION2A28 - 431
3X-RAY DIFFRACTION3C28 - 431
4X-RAY DIFFRACTION4D28 - 431

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