[English] 日本語
Yorodumi
- PDB-6zz9: Crystal structure of CbpB from Streptococcus agalactiae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zz9
TitleCrystal structure of CbpB from Streptococcus agalactiae
ComponentsCBS domain-containing protein
KeywordsSIGNALING PROTEIN / CBS / c-di-AMP
Function / homologyCBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / : / CBS domain-containing protein
Function and homology information
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.644 Å
AuthorsMechaly, A.E. / Covaleda-Cortes, G. / Kaminski, P.A.
CitationJournal: Febs J. / Year: 2023
Title: The c-di-AMP-binding protein CbpB modulates the level of ppGpp alarmone in Streptococcus agalactiae.
Authors: Covaleda-Cortes, G. / Mechaly, A. / Brissac, T. / Baehre, H. / Devaux, L. / England, P. / Raynal, B. / Hoos, S. / Gominet, M. / Firon, A. / Trieu-Cuot, P. / Kaminski, P.A.
History
DepositionAug 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CBS domain-containing protein
B: CBS domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3757
Polymers39,6972
Non-polymers6785
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-122 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.61, 60.61, 190.47
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein CBS domain-containing protein / FIG042801: CBS domain containing protein


Mass: 19848.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria)
Gene: ykuL, C6N06_01440, D5F95_08070, DX05_08405, E8E04_03435, F5F86_02645, NCTC9828_00932, WA02_02795, WA05_04310
Production host: Escherichia coli (E. coli) / References: UniProt: A0A076YWK5
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 200 mM ammonium sulfate, 100 mM MES pH 6.5, 30% w/v PEG MME 5000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0716 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0716 Å / Relative weight: 1
ReflectionResolution: 2.644→47.62 Å / Num. obs: 11037 / % possible obs: 98.94 % / Redundancy: 4.3 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.06712 / Rpim(I) all: 0.03644 / Rrim(I) all: 0.07653 / Net I/σ(I): 10.76
Reflection shellResolution: 2.644→2.739 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.346 / Num. unique obs: 1030 / CC1/2: 0.709 / CC star: 0.911 / Rpim(I) all: 0.7379 / Rrim(I) all: 1.538 / % possible all: 96.34

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
AutoSolphasing
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.644→47.62 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 1.075 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.586 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.321
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 551 -RANDOM
Rwork0.2331 ---
obs0.2341 11003 99.2 %-
Displacement parametersBiso mean: 100.59 Å2
Baniso -1Baniso -2Baniso -3
1--13.357 Å20 Å20 Å2
2---13.357 Å20 Å2
3---26.714 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.644→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 17 0 2542
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072589HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.893518HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d895SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes429HARMONIC5
X-RAY DIFFRACTIONt_it2589HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion368SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1902SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion17.66
LS refinement shellResolution: 2.644→2.68 Å
RfactorNum. reflection% reflection
Rfree0.4351 21 -
Rwork0.3025 --
obs--92.69 %
Refinement TLS params.

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)
10.824-0.4223-2.22730-1.10083.430.01140.1423-0.12840.14230.04630.1058-0.12840.1058-0.05770.1488-0.1475-0.083-0.0113-0.0151-0.027728.643833.6122.275
20.8777-0.77081.49680.6128-1.12792.443-0.031-0.09170.4106-0.09170.0426-0.08430.4106-0.0843-0.01160.1356-0.152-0.0636-0.12520.04460.00629.942325.600219.8683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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