[English] 日本語
Yorodumi
- PDB-5f7m: Blood group antigen binding adhesin BabA of Helicobacter pylori s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f7m
TitleBlood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with blood group H Lewis b hexasaccharide
Components
  • Adhesin binding fucosylated histo-blood group antigen
  • Nanobody Nb-ER19
KeywordsCELL ADHESION / Adhesin / Lectin / Nanobody / Complex
Function / homologySabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Adhesin binding fucosylated histo-blood group antigen
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsMoonens, K. / Gideonsson, P. / Subedi, S. / Romao, E. / Oscarson, S. / Muyldermans, S. / Boren, T. / Remaut, H.
Funding support Belgium, Sweden, 6items
OrganizationGrant numberCountry
Flanders Institute of Biotechnology (VIB)PRJ9 Belgium
Flanders Science Foundation (FWO)Odysseus program Belgium
Hercules FoundationUABR/09/005 Belgium
Vetenskapsradet/VR Sweden
Cancerfonden Sweden
CitationJournal: Cell Host Microbe / Year: 2016
Title: Structural Insights into Polymorphic ABO Glycan Binding by Helicobacter pylori.
Authors: Moonens, K. / Gideonsson, P. / Subedi, S. / Bugaytsova, J. / Romao, E. / Mendez, M. / Norden, J. / Fallah, M. / Rakhimova, L. / Shevtsova, A. / Lahmann, M. / Castaldo, G. / Brannstrom, K. / ...Authors: Moonens, K. / Gideonsson, P. / Subedi, S. / Bugaytsova, J. / Romao, E. / Mendez, M. / Norden, J. / Fallah, M. / Rakhimova, L. / Shevtsova, A. / Lahmann, M. / Castaldo, G. / Brannstrom, K. / Coppens, F. / Lo, A.W. / Ny, T. / Solnick, J.V. / Vandenbussche, G. / Oscarson, S. / Hammarstrom, L. / Arnqvist, A. / Berg, D.E. / Muyldermans, S. / Boren, T. / Remaut, H.
History
DepositionDec 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adhesin binding fucosylated histo-blood group antigen
B: Adhesin binding fucosylated histo-blood group antigen
C: Nanobody Nb-ER19
D: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,2606
Polymers125,2604
Non-polymers2,0002
Water2,702150
1
A: Adhesin binding fucosylated histo-blood group antigen
C: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6303
Polymers62,6302
Non-polymers1,0001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint18 kcal/mol
Surface area23710 Å2
MethodPISA
2
B: Adhesin binding fucosylated histo-blood group antigen
D: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6303
Polymers62,6302
Non-polymers1,0001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint19 kcal/mol
Surface area23810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.096, 131.889, 123.102
Angle α, β, γ (deg.)90.00, 94.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNGLYGLYAA35 - 46133 - 459
21ASNASNGLYGLYBB35 - 46133 - 459
12VALVALSERSERCC3 - 1142 - 113
22VALVALSERSERDD3 - 1142 - 113

NCS ensembles :
ID
1
2

-
Components

#1: Protein Adhesin binding fucosylated histo-blood group antigen


Mass: 49369.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: babA2 / Variant: 17875 / Production host: Escherichia coli (E. coli) / Variant (production host): Top10 / References: UniProt: O52269
#2: Antibody Nanobody Nb-ER19


Mass: 13260.856 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Variant (production host): Top10
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 999.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3[LFucpa1-4]DGlcpNAcb1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-2-4-4/a4-b1_b3-c1_c3-d1_c4-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}[(4+1)][a-L-Fucp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M sodium nitrate, 0.1M Bis Tris propane pH 6.5, 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.72→45 Å / Num. obs: 43591 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.7
Reflection shellResolution: 2.72→2.89 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

-
Processing

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

5f7k


Resolution: 2.72→45 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 22.627 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.496 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21767 2194 5 %RANDOM
Rwork0.17898 ---
obs0.18098 41291 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.465 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å20.53 Å2
2--0.95 Å20 Å2
3----1.95 Å2
Refinement stepCycle: 1 / Resolution: 2.72→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7974 0 136 150 8260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.028262
X-RAY DIFFRACTIONr_bond_other_d0.0040.027666
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.96611248
X-RAY DIFFRACTIONr_angle_other_deg0.992317622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68251060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01826.034348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.925151322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4711526
X-RAY DIFFRACTIONr_chiral_restr0.0820.21326
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219536
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021846
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_it1.9042.6164258
X-RAY DIFFRACTIONr_mcbond_other1.9042.6164257
X-RAY DIFFRACTIONr_mcangle_it3.1813.9215312
X-RAY DIFFRACTIONr_mcangle_other3.1813.9225313
X-RAY DIFFRACTIONr_scbond_it2.6132.8754004
X-RAY DIFFRACTIONr_scbond_other2.6122.8754005
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2484.1925937
X-RAY DIFFRACTIONr_long_range_B_refined5.9420.6939227
X-RAY DIFFRACTIONr_long_range_B_other5.91220.6759206
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A232950.09
12B232950.09
21C66060.05
22D66060.05
LS refinement shellResolution: 2.72→2.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 162 -
Rwork0.293 3008 -
obs--99 %
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)
11.29611.4416-0.93874.3847-2.01731.68410.0576-0.05520.10690.03580.02270.2004-0.0505-0.0234-0.08030.06650.0491-0.01940.1453-0.0560.03246.9471-19.621218.1547
21.313-1.44581.1433.9553-2.0381.97870.0694-0.1068-0.1570.13170.14010.28920.2556-0.1199-0.20950.1861-0.05720.01290.1487-0.07170.08049.361927.010839.7351
32.27850.17920.93986.0565-2.38194.1657-0.0947-0.0554-0.18240.34060.0459-0.2693-0.08130.16390.04880.18640.0117-0.04490.1132-0.0050.035712.0852-42.197845.0595
42.76840.4279-0.61425.4694-2.67584.0198-0.1364-0.07090.2482-0.1429-0.0044-0.36820.14990.12960.14080.0306-0.01690.01940.0337-0.03270.078118.962950.938615.2299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 462
2X-RAY DIFFRACTION2B35 - 463
3X-RAY DIFFRACTION3C3 - 115
4X-RAY DIFFRACTION4D3 - 116

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more