[English] 日本語
Yorodumi
- PDB-5h6i: Crystal Structure of GBS CAMP Factor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5h6i
TitleCrystal Structure of GBS CAMP Factor
ComponentsProtein B
KeywordsTOXIN / Pore forming toxin
Function / homologyCAMP factor / CAMP factor (Cfa) / IgG binding / extracellular region / Protein B
Function and homology information
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsJin, T.C. / Brefo-Mensah, E.K.
CitationJournal: J.Biol.Chem. / Year: 2018
Title: Crystal structure of theStreptococcus agalactiaeCAMP factor provides insights into its membrane-permeabilizing activity.
Authors: Jin, T. / Brefo-Mensah, E. / Fan, W. / Zeng, W. / Li, Y. / Zhang, Y. / Palmer, M.
History
DepositionNov 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein B
B: Protein B
C: Protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4367
Polymers81,1123
Non-polymers3244
Water63135
1
A: Protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2654
Polymers27,0371
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein B


Theoretical massNumber of molelcules
Total (without water)27,0371
Polymers27,0371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1342
Polymers27,0371
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.950, 116.050, 72.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-301-

SO4

21A-302-

SO4

-
Components

#1: Protein Protein B / cAMP factor


Mass: 27037.498 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P09879
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2M NH4NO3, 20% PEG 3350, 0.1 M MES pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 54560 / % possible obs: 99.6 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.4
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.34 / CC1/2: 0.784 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIXdev_2481refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→48.917 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.96
RfactorNum. reflection% reflection
Rfree0.285 3779 6.93 %
Rwork0.2337 --
obs0.2372 54560 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→48.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4956 0 28 35 5019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025033
X-RAY DIFFRACTIONf_angle_d0.4356821
X-RAY DIFFRACTIONf_dihedral_angle_d5.0523135
X-RAY DIFFRACTIONf_chiral_restr0.035840
X-RAY DIFFRACTIONf_plane_restr0.003871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4502-2.48120.42281360.39321795X-RAY DIFFRACTION96
2.4812-2.51380.42531400.33921876X-RAY DIFFRACTION100
2.5138-2.54830.32771380.33511858X-RAY DIFFRACTION100
2.5483-2.58470.38171440.3061942X-RAY DIFFRACTION100
2.5847-2.62330.36761390.31291843X-RAY DIFFRACTION100
2.6233-2.66420.3971360.3171889X-RAY DIFFRACTION100
2.6642-2.70790.37851420.30251903X-RAY DIFFRACTION100
2.7079-2.75460.42951360.30361855X-RAY DIFFRACTION100
2.7546-2.80470.38561440.29691898X-RAY DIFFRACTION100
2.8047-2.85860.28821430.28961881X-RAY DIFFRACTION100
2.8586-2.9170.34431420.30021937X-RAY DIFFRACTION100
2.917-2.98040.37731360.28961825X-RAY DIFFRACTION100
2.9804-3.04970.30421410.31391917X-RAY DIFFRACTION100
3.0497-3.1260.33261430.29041883X-RAY DIFFRACTION100
3.126-3.21050.36821410.27781866X-RAY DIFFRACTION100
3.2105-3.30490.33291410.27311881X-RAY DIFFRACTION100
3.3049-3.41160.34121410.26611884X-RAY DIFFRACTION100
3.4116-3.53350.35531380.25981874X-RAY DIFFRACTION100
3.5335-3.67490.2551420.24531889X-RAY DIFFRACTION100
3.6749-3.84210.28361360.22861887X-RAY DIFFRACTION100
3.8421-4.04460.25351420.21791880X-RAY DIFFRACTION100
4.0446-4.29780.28471390.1961908X-RAY DIFFRACTION100
4.2978-4.62940.26181400.19141861X-RAY DIFFRACTION100
4.6294-5.09490.25261420.18811902X-RAY DIFFRACTION100
5.0949-5.83110.26351380.22241872X-RAY DIFFRACTION100
5.8311-7.34260.27141390.22791899X-RAY DIFFRACTION100
7.3426-48.92720.16811400.15461876X-RAY DIFFRACTION100

+
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