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- PDB-6gw5: X-ray structure of the Helicobacter pylori SabA adhesin domain -

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Basic information

Entry
Database: PDB / ID: 6gw5
TitleX-ray structure of the Helicobacter pylori SabA adhesin domain
ComponentsPutative Outer membrane protein
KeywordsCELL ADHESION / Helicobacter pylori / adhesin / outer membrane protein / Lewis X / lectin
Function / homologyOuter 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: 2.52 Å
AuthorsCoppens, F. / Remaut, H.
Funding support Belgium, 1items
OrganizationGrant numberCountry
G.0902.09 Belgium
CitationJournal: Mol. Microbiol. / Year: 2018
Title: Hop-family Helicobacter outer membrane adhesins form a novel class of Type 5-like secretion proteins with an interrupted beta-barrel domain.
Authors: Coppens, F. / Castaldo, G. / Debraekeleer, A. / Subedi, S. / Moonens, K. / Lo, A. / Remaut, H.
History
DepositionJun 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 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 / 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 1.3Oct 23, 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
A: Putative Outer membrane protein
B: Putative Outer membrane protein


Theoretical massNumber of molelcules
Total (without water)97,3382
Polymers97,3382
Non-polymers00
Water2,810156
1
A: Putative Outer membrane protein


Theoretical massNumber of molelcules
Total (without water)48,6691
Polymers48,6691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative Outer membrane protein


Theoretical massNumber of molelcules
Total (without water)48,6691
Polymers48,6691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.146, 87.321, 169.007
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 23 - 438 / Label seq-ID: 2 - 417

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

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Components

#1: Protein Putative Outer membrane protein


Mass: 48668.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: jhp_0662 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9ZLB8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 15% PEG 3350, 0.2 M KF, 0.1 M citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.52→47.5 Å / Num. obs: 140735 / % possible obs: 97 % / Redundancy: 4 % / Biso Wilson estimate: 45.2 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.119 / Net I/av σ(I): 11.78 / Net I/σ(I): 11.8
Reflection shellResolution: 2.52→2.59 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 10599 / CC1/2: 0.79 / Rrim(I) all: 0.897 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O5J

4o5j


Resolution: 2.52→47.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.489 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.473 / ESU R Free: 0.29 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25565 1716 5 %RANDOM
Rwork0.20217 ---
obs0.20477 32620 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.51 Å2
Baniso -1Baniso -2Baniso -3
1-4.07 Å20 Å20 Å2
2---1.16 Å20 Å2
3----2.9 Å2
Refinement stepCycle: 1 / Resolution: 2.52→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 0 0 156 6242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.026182
X-RAY DIFFRACTIONr_bond_other_d0.0060.025839
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.948408
X-RAY DIFFRACTIONr_angle_other_deg1.371313388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5885774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.98327.4300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.565151047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg32.805154
X-RAY DIFFRACTIONr_chiral_restr0.0950.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027267
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021429
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_it4.1745.2743126
X-RAY DIFFRACTIONr_mcbond_other4.1745.2723125
X-RAY DIFFRACTIONr_mcangle_it6.2677.8823890
X-RAY DIFFRACTIONr_mcangle_other6.2667.8843891
X-RAY DIFFRACTIONr_scbond_it4.5465.6353056
X-RAY DIFFRACTIONr_scbond_other4.5455.6363057
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0028.2724519
X-RAY DIFFRACTIONr_long_range_B_refined10.37949.27227111
X-RAY DIFFRACTIONr_long_range_B_other10.37949.28327074
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 45050 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 127 -
Rwork0.318 2412 -
obs--98.14 %

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