[English] 日本語
Yorodumi
- PDB-7c7r: Biofilm associated protein - B domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c7r
TitleBiofilm associated protein - B domain
ComponentsBiofilm-associated surface protein
KeywordsCELL ADHESION / Cell wall-anchored surface protein / biofilm formation
Function / homology
Function and homology information


cell-abiotic substrate adhesion / single-species submerged biofilm formation / cell-cell adhesion / membrane
Similarity search - Function
Bacterial Ig domain / Bacterial Ig domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Biofilm-associated surface protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.07 Å
AuthorsMa, J.F. / Xu, Z.H. / Zhang, Y.K. / Cheng, X. / Fan, S.L. / Wang, J.W. / Fang, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31872712 China
Citation
Journal: Embo J. / Year: 2021
Title: Structural mechanism for modulation of functional amyloid and biofilm formation by Staphylococcal Bap protein switch.
Authors: Ma, J. / Cheng, X. / Xu, Z. / Zhang, Y. / Valle, J. / Fan, S. / Zuo, X. / Lasa, I. / Fang, X.
#1: Journal: To Be Published
Title: Integrative structure and functional implications of a 236-kDa modular protein Bap from Staphylococcus aureus
Authors: Ma, J.F. / Zhang, Y.K. / Cheng, X. / Fan, S.L. / Xu, N. / Fang, X.Y.
History
DepositionMay 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Author supporting evidence / Database references / Structure summary
Category: citation_author / pdbx_audit_support / struct_keywords
Item: _pdbx_audit_support.grant_number / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Jun 2, 2021Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Jul 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Biofilm-associated surface protein
A: Biofilm-associated surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,93512
Polymers99,5352
Non-polymers40110
Water54030
1
B: Biofilm-associated surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9686
Polymers49,7671
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-12 kcal/mol
Surface area18040 Å2
MethodPISA
2
A: Biofilm-associated surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9686
Polymers49,7671
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.171, 171.171, 102.503
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))
21(chain B and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))A361 - 547
121(chain A and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))A549 - 775
131(chain A and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))A801 - 805
211(chain B and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))B361 - 547
221(chain B and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))B549 - 775
231(chain B and (resid 361 through 547 or resid 549 through 775 or resid 801 through 805))B801 - 805

-
Components

#1: Protein Biofilm-associated surface protein


Mass: 49767.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: bap / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): B834 / References: UniProt: Q79LN3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.06 Å3/Da / Density % sol: 69.67 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium Cacodylate pH 6.5, 40% MPD, 5% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 3.07→49.1 Å / Num. obs: 27970 / % possible obs: 96.42 % / Redundancy: 2 % / Biso Wilson estimate: 76.02 Å2 / CC1/2: 0.999 / Net I/σ(I): 25.33
Reflection shellResolution: 3.07→3.18 Å / Num. unique obs: 2317 / CC1/2: 0.661

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
STARANISOdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.07→49.1 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 1399 5 %
Rwork0.1918 26569 -
obs0.1935 27968 96.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.71 Å2 / Biso mean: 71.6052 Å2 / Biso min: 25.82 Å2
Refinement stepCycle: final / Resolution: 3.07→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6480 0 10 30 6520
Biso mean--68.17 55.01 -
Num. residues----830
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2492X-RAY DIFFRACTION4.314TORSIONAL
12B2492X-RAY DIFFRACTION4.314TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.07-3.180.33541160.2882200231682
3.18-3.310.29491230.27052354247787
3.31-3.460.27431370.22222582271996
3.46-3.640.261430.209427142857100
3.64-3.870.25851430.188827282871100
3.87-4.170.21671440.179827352879100
4.17-4.580.17591450.144327392884100
4.59-5.250.15721450.148227702915100
5.25-6.610.22661480.205628022950100
6.61-49.850.23081550.204329453100100
Refinement TLS params.Method: refined / Origin x: 139.4015 Å / Origin y: 62.7425 Å / Origin z: 24.636 Å
111213212223313233
T0.2948 Å2-0.0356 Å20.0557 Å2-0.3623 Å2-0.0108 Å2--0.2829 Å2
L0.6057 °20.2265 °20.0894 °2-0.8434 °2-0.1489 °2--0.48 °2
S0.0103 Å °0.0148 Å °0.0587 Å °0.0856 Å °0.0364 Å °0.0781 Å °-0.14 Å °0.0452 Å °-0.0009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB361 - 775
2X-RAY DIFFRACTION1allB801 - 910
3X-RAY DIFFRACTION1allA361 - 775
4X-RAY DIFFRACTION1allA801 - 922

+
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