[English] 日本語
Yorodumi
- PDB-5vaf: Crystal structure of accessory secretion protein 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vaf
TitleCrystal structure of accessory secretion protein 1
ComponentsAccessory Sec system protein Asp1
KeywordsCELL ADHESION / O-glycosylation / bacterial adhesin / accessory secretion
Function / homologyAccessory secretory system protein Asp1 / Accessory Sec system protein Asp1 / protein transport / Accessory Sec system protein Asp1
Function and homology information
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.771 Å
AuthorsChen, Y. / Rapoport, T.A. / Jeffrey, P.D.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM052586 United States
Helen Hay Whitney Foundation United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Unraveling the sequence of cytosolic reactions in the export of GspB adhesin fromStreptococcus gordonii.
Authors: Chen, Y. / Bensing, B.A. / Seepersaud, R. / Mi, W. / Liao, M. / Jeffrey, P.D. / Shajahan, A. / Sonon, R.N. / Azadi, P. / Sullam, P.M. / Rapoport, T.A.
History
DepositionMar 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.6Oct 4, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Accessory Sec system protein Asp1
B: Accessory Sec system protein Asp1
C: Accessory Sec system protein Asp1
D: Accessory Sec system protein Asp1


Theoretical massNumber of molelcules
Total (without water)253,1974
Polymers253,1974
Non-polymers00
Water543
1
A: Accessory Sec system protein Asp1


Theoretical massNumber of molelcules
Total (without water)63,2991
Polymers63,2991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Accessory Sec system protein Asp1


Theoretical massNumber of molelcules
Total (without water)63,2991
Polymers63,2991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Accessory Sec system protein Asp1


Theoretical massNumber of molelcules
Total (without water)63,2991
Polymers63,2991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Accessory Sec system protein Asp1


Theoretical massNumber of molelcules
Total (without water)63,2991
Polymers63,2991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.502, 99.897, 179.069
Angle α, β, γ (deg.)100.660, 90.070, 95.780
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Accessory Sec system protein Asp1 / Accessory secretory protein Asp1 / Orf1


Mass: 63299.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Gene: asp1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AET9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 100 mM Bis-Tris Propane pH 9.2 28% PEG6000

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.77→97.654 Å / Num. obs: 66446 / % possible obs: 92.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 46.43 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 13.63

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VAE
Resolution: 2.771→97.654 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.93
RfactorNum. reflection% reflection
Rfree0.2816 3344 5.05 %
Rwork0.2083 --
obs0.212 66159 92.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.5 Å2 / Biso mean: 50.5684 Å2 / Biso min: 15.41 Å2
Refinement stepCycle: final / Resolution: 2.771→97.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17257 0 0 3 17260
Biso mean---33.14 -
Num. residues----2052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917690
X-RAY DIFFRACTIONf_angle_d1.06923971
X-RAY DIFFRACTIONf_chiral_restr0.0562558
X-RAY DIFFRACTIONf_plane_restr0.0063094
X-RAY DIFFRACTIONf_dihedral_angle_d4.50210491
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7712-2.81080.41911230.33662558268192
2.8108-2.85280.41351360.31372575271192
2.8528-2.89730.38691450.28522542268790
2.8973-2.94480.3721350.2562621275690
2.9448-2.99560.36211290.24952482261189
2.9956-3.05010.33171170.24722411252886
3.0501-3.10880.30171400.2522532267289
3.1088-3.17220.36351590.25682679283894
3.1722-3.24120.3341310.2652718284996
3.2412-3.31660.40981390.24872665280496
3.3166-3.39960.33411510.2342682283395
3.3996-3.49150.30351420.2312709285195
3.4915-3.59420.29161460.21142616276294
3.5942-3.71020.2981530.21082614276792
3.7102-3.84280.29251190.1952588270791
3.8428-3.99670.28071740.17782650282496
3.9967-4.17860.21481310.17192748287995
4.1786-4.39890.21481410.16382645278696
4.3989-4.67450.2291160.1612673278993
4.6745-5.03540.24631320.1662496262889
5.0354-5.54210.22371470.18132705285296
5.5421-6.34390.27011380.20082680281895
6.3439-7.99210.2491590.20562571273091
7.9921-97.71510.23261410.20012655279694

+
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