[English] 日本語
Yorodumi
- PDB-6lxh: Staphylococcus aureus surface protein-sdrc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lxh
TitleStaphylococcus aureus surface protein-sdrc
ComponentsSer-Asp rich fibrinogen-binding, bone sialoprotein-binding protein
KeywordsSURFACTANT PROTEIN / CWA protein / self-association / biofilm accumulation / sdrc
Function / homology
Function and homology information


cell adhesion / extracellular region
Similarity search - Function
SD-repeat containing protein, B domain / SdrD B-like domain / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide ...SD-repeat containing protein, B domain / SdrD B-like domain / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / 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
Serine-aspartate repeat-containing protein C / Ser-Asp rich fibrinogen-binding, bone sialoprotein-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsPi, Y. / Ji, Q.
CitationJournal: Biochemistry / Year: 2020
Title: Structural Basis ofStaphylococcus aureusSurface Protein SdrC.
Authors: Pi, Y. / Chen, W. / Ji, Q.
History
DepositionFeb 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 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: Ser-Asp rich fibrinogen-binding, bone sialoprotein-binding protein
B: Ser-Asp rich fibrinogen-binding, bone sialoprotein-binding protein
C: Ser-Asp rich fibrinogen-binding, bone sialoprotein-binding protein


Theoretical massNumber of molelcules
Total (without water)108,0373
Polymers108,0373
Non-polymers00
Water15,547863
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-4 kcal/mol
Surface area41170 Å2
Unit cell
Length a, b, c (Å)61.753, 120.333, 130.343
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ser-Asp rich fibrinogen-binding, bone sialoprotein-binding protein / cell-wall anchored protein


Mass: 36012.180 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: sdrC / Production host: Escherichia coli (E. coli) / References: UniProt: Q2UWJ6, UniProt: Q2G0L5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 863 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7 / Details: 0.1M HEPES, 30% Jeffamine ED-2001, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Apr 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.07→88.42 Å / Num. obs: 59835 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.956 / Net I/σ(I): 88.42
Reflection shellResolution: 2.07→2.123 Å / Num. unique obs: 4110 / CC1/2: 0.956

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→88.42 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.407 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 3021 5 %RANDOM
Rwork0.1699 ---
obs0.1729 56852 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.67 Å2 / Biso mean: 30.314 Å2 / Biso min: 7.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å2-0 Å20 Å2
2--0.78 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 2.07→88.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7354 0 0 863 8217
Biso mean---35 -
Num. residues----920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.027494
X-RAY DIFFRACTIONr_bond_other_d0.0020.026781
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.92610168
X-RAY DIFFRACTIONr_angle_other_deg1.004315625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.135913
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51826.114386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.266151271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.031515
X-RAY DIFFRACTIONr_chiral_restr0.1080.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021782
LS refinement shellResolution: 2.07→2.123 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.249 220 -
Rwork0.196 4110 -
obs--99.15 %

+
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