[English] 日本語
Yorodumi
- PDB-5f93: Blood group antigen binding adhesin BabA of Helicobacter pylori s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f93
TitleBlood group antigen binding adhesin BabA of Helicobacter pylori strain A730 in complex with blood group H Lewis b hexasaccharide
Components
  • Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
  • Nanobody Nb-ER19
KeywordsCELL ADHESION / Adhesin / Lectin / Nanobody / Complex
Function / homology
Function and homology information


SabA, 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
Similarity search - Domain/homology
Adhesin binding fucosylated histo-blood group antigen / Adhesin
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsMoonens, K. / Gideonsson, P. / Subedi, S. / Romao, E. / Oscarson, S. / Muyldermans, S. / Boren, T. / Remaut, H.
Funding support Belgium, Sweden, 5items
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 9, 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)256,87412
Polymers252,8758
Non-polymers4,0004
Water75742
1
A: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
C: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2193
Polymers63,2192
Non-polymers1,0001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint19 kcal/mol
Surface area24330 Å2
MethodPISA
2
B: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
D: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2193
Polymers63,2192
Non-polymers1,0001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint19 kcal/mol
Surface area24570 Å2
MethodPISA
3
E: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
F: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2193
Polymers63,2192
Non-polymers1,0001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint21 kcal/mol
Surface area24190 Å2
MethodPISA
4
G: Adhesin binding fucosylated histo-blood group antigen,Adhesin,Adhesin binding fucosylated histo-blood group antigen
H: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2193
Polymers63,2192
Non-polymers1,0001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint19 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.175, 134.473, 123.979
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 49957.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: In this hybrid construct the insertion domain (residues 179-258) of the Alaskan strain A730, responsible for carbohydrate binding, was grafted into the framework of the generalist strain 17875
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: babA2, babA / Production host: Escherichia coli (E. coli) / Variant (production host): Top10 / References: UniProt: O52269, UniProt: Q6DSX7
#2: Antibody
Nanobody Nb-ER19


Mass: 13260.856 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#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)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 999.912 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3[LFucpa1-4]DGlcpNAcb1-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1a_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
[][a-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.: 42 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2- Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1 M Buffer System 2 (Sodium HEPES; MOPS (acid)) pH ...Details: 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2- Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 0.1 M Buffer System 2 (Sodium HEPES; MOPS (acid)) pH 7.5, 50 % v/v EDO_P8K (40% v/v Ethylene glycol; 20 % w/v PEG 8000

-
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: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.99→48.64 Å / Num. obs: 65294 / % possible obs: 97.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.9
Reflection shellResolution: 2.99→3.16 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.7 / % possible all: 86.1

-
Processing

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

5f7k


Resolution: 2.99→48.64 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 38.088 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23381 3241 5 %RANDOM
Rwork0.18107 ---
obs0.18371 62025 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.088 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20.01 Å2
2---0.71 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 2.99→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16179 0 272 42 16493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216788
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215483
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.96522861
X-RAY DIFFRACTIONr_angle_other_deg0.819335587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37552139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37526.138738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.537152672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5051548
X-RAY DIFFRACTIONr_chiral_restr0.0790.22666
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023788
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_it3.425.0848583
X-RAY DIFFRACTIONr_mcbond_other3.4185.0848582
X-RAY DIFFRACTIONr_mcangle_it5.5547.61210704
X-RAY DIFFRACTIONr_mcangle_other5.5547.61210705
X-RAY DIFFRACTIONr_scbond_it3.9815.598205
X-RAY DIFFRACTIONr_scbond_other3.9815.598206
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.528.2112155
X-RAY DIFFRACTIONr_long_range_B_refined8.69640.38918612
X-RAY DIFFRACTIONr_long_range_B_other8.69640.39118613
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.994→3.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 166 -
Rwork0.362 3371 -
obs--72.2 %
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)
10.4649-0.382-0.28871.15280.51390.30540.0491-0.07350.0647-0.10750.0264-0.0156-0.02630.02-0.07560.0620.0013-0.02170.36380.01670.071380.4099-14.6344163.9437
20.3735-0.4452-0.22590.96840.42430.24020.0954-0.20120.0161-0.1311-0.0329-0.0249-0.05560.0713-0.06250.0485-0.0674-0.00690.4014-0.02330.0709131.5747-24.8859164.8912
30.09010.19320.20840.92380.5170.53790.036-0.0182-0.0347-0.06910.1083-0.15120.11490.0216-0.14440.12690.0494-0.03690.31340.02270.12489.111334.5943144.2087
40.07630.30480.1391.39460.74320.6474-0.0089-0.0355-0.03370.06140.0096-0.16940.18020.0303-0.00080.11660.04060.00970.34640.0360.1055141.159125.2084143.211
50.7086-0.4465-0.40781.82160.9961.85910.0266-0.1139-0.1304-0.47410.0330.2215-0.0246-0.0072-0.05960.2412-0.0092-0.12360.32810.01020.09778.3721-38.0614137.3858
61.1918-0.6643-0.65211.72551.58972.0980.0734-0.0711-0.0603-0.418-0.11730.0906-0.08790.00760.04390.25710.0393-0.04340.27490.01230.0102130.6266-47.5089137.7382
70.63530.2618-0.40520.7420.50041.29080.037-0.13810.0045-0.01550.06990.04360.00890.0682-0.10690.04570.0573-0.02270.44760.10560.176.042256.5173168.7193
80.29730.16120.25881.28261.16241.6932-0.0019-0.0770.07190.0398-0.00750.02790.1486-0.10550.00940.02970.0052-0.00740.44390.07380.0504129.152546.5957168.3661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 467
2X-RAY DIFFRACTION2B32 - 466
3X-RAY DIFFRACTION3E32 - 466
4X-RAY DIFFRACTION4G32 - 466
5X-RAY DIFFRACTION5C3 - 116
6X-RAY DIFFRACTION6D3 - 116
7X-RAY DIFFRACTION7F3 - 116
8X-RAY DIFFRACTION8H3 - 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