[English] 日本語
Yorodumi
- PDB-5boa: Crystal Structure of the Meningitis Pathogen Streptococcus suis a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5boa
TitleCrystal Structure of the Meningitis Pathogen Streptococcus suis adhesion Fhb bound to the disaccharide receptor Gb2
ComponentsTranslation initiation factor 2 (IF-2 GTPase)
KeywordsSUGAR BINDING PROTEIN / protein-polysaccharide complex
Function / homologyfibrinogen binding / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / translation initiation factor activity / peptidoglycan-based cell wall / membrane / Translation initiation factor 2 (IF-2 GTPase)
Function and homology information
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.708 Å
Model detailssandwich core
AuthorsZhang, C. / Yu, Y. / Yang, M. / Jiang, Y.
CitationJournal: Febs Lett. / Year: 2016
Title: Structural basis of the interaction between the meningitis pathogen Streptococcus suis adhesin Fhb and its human receptor.
Authors: Zhang, C. / Hao, H. / Yu, Y. / Kong, D. / Chen, S. / Jiang, H. / Yuan, Y. / Zheng, Y. / Yang, M. / Jiang, Y.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / 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 / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: 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: Translation initiation factor 2 (IF-2 GTPase)
B: Translation initiation factor 2 (IF-2 GTPase)
C: Translation initiation factor 2 (IF-2 GTPase)
D: Translation initiation factor 2 (IF-2 GTPase)
E: Translation initiation factor 2 (IF-2 GTPase)
F: Translation initiation factor 2 (IF-2 GTPase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,55912
Polymers153,5056
Non-polymers2,0546
Water00
1
A: Translation initiation factor 2 (IF-2 GTPase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9262
Polymers25,5841
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Translation initiation factor 2 (IF-2 GTPase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9262
Polymers25,5841
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Translation initiation factor 2 (IF-2 GTPase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9262
Polymers25,5841
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Translation initiation factor 2 (IF-2 GTPase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9262
Polymers25,5841
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Translation initiation factor 2 (IF-2 GTPase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9262
Polymers25,5841
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Translation initiation factor 2 (IF-2 GTPase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9262
Polymers25,5841
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.488, 136.574, 75.551
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Translation initiation factor 2 (IF-2 GTPase)


Mass: 25584.186 Da / Num. of mol.: 6 / Fragment: ligand binding domain (UNP RESIDUES 39-343)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (strain 05ZYH33) (bacteria)
Strain: 05ZYH33 / Gene: SSU05_0272 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4VT01
#2: Polysaccharide
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2112h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][a-D-Galp]{}}LINUCSPDB-CARE

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 3350, NH4Ac

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 36259 / % possible obs: 100 % / Redundancy: 21.6 % / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.044 / Rrim(I) all: 0.203 / Χ2: 1.994 / Net I/av σ(I): 25.6 / Net I/σ(I): 5.6 / Num. measured all: 782182
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
2.7-2.7521.70.89517760.9460.1950.9161.1
2.75-2.821.60.79417760.9580.1740.8131.115
2.8-2.8521.70.72117710.9640.1570.7381.116
2.85-2.9121.70.61117910.970.1330.6261.254
2.91-2.9721.70.54417920.9770.1190.5571.169
2.97-3.0421.70.48417870.9790.1060.4951.247
3.04-3.1221.80.39818030.9880.0870.4071.29
3.12-3.221.80.32617680.990.0710.3341.42
3.2-3.321.80.29717960.9920.0650.3041.61
3.3-3.421.80.30318270.9930.0670.311.798
3.4-3.5221.80.43317750.9890.0960.4444.324
3.52-3.6621.70.30917900.9930.0670.3163.552
3.66-3.8321.60.17518140.9960.0390.182.07
3.83-4.0321.50.26718120.9950.0580.2734.303
4.03-4.2921.40.11218120.9980.0250.1151.754
4.29-4.62210.08718300.9990.0190.0891.486
4.62-5.0821.10.07918350.9990.0170.0811.292
5.08-5.8122.10.08318440.9990.0180.0851.265
5.81-7.3221.80.08418690.9990.0180.0861.219
7.32-5020.40.05519910.9940.0130.0575.412

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BOB

5bob


Resolution: 2.708→48.495 Å / FOM work R set: 0.7946 / SU ML: 0.36 / σ(F): 1.35 / Phase error: 26.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2641 1805 4.99 %
Rwork0.1905 34385 -
obs0.1942 36190 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.59 Å2 / Biso mean: 40.05 Å2 / Biso min: 18.7 Å2
Refinement stepCycle: final / Resolution: 2.708→48.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9277 0 138 0 9415
Biso mean--36.58 --
Num. residues----1169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089612
X-RAY DIFFRACTIONf_angle_d1.19113050
X-RAY DIFFRACTIONf_chiral_restr0.0471490
X-RAY DIFFRACTIONf_plane_restr0.0051651
X-RAY DIFFRACTIONf_dihedral_angle_d15.9053404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7078-2.7810.32181230.24132454257794
2.781-2.86280.34281370.237426072744100
2.8628-2.95520.32511510.227826232774100
2.9552-3.06080.33571420.223226082750100
3.0608-3.18330.31251370.211826402777100
3.1833-3.32820.28261360.195926282764100
3.3282-3.50360.33871330.204126312764100
3.5036-3.7230.27131340.194926552789100
3.723-4.01030.23741390.187626472786100
4.0103-4.41370.23211260.16526622788100
4.4137-5.05180.20531570.155526942851100
5.0518-6.36240.23421330.187127012834100
6.3624-48.50310.24911570.182228352992100

+
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://pdbjlvh1.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