[English] 日本語
Yorodumi
- PDB-1c76: STAPHYLOKINASE (SAK) MONOMER -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c76
TitleSTAPHYLOKINASE (SAK) MONOMER
ComponentsSTAPHYLOKINASE
KeywordsHYDROLASE / BETA-GRASP FAMILY
Function / homology
Function and homology information


symbiont-mediated activation of host plasminogen / symbiont-mediated suppression of host complement activation by activation of host proteases / extracellular region
Similarity search - Function
Ubiquitin-like (UB roll) - #130 / Staphylokinase / Staphylokinase/Streptokinase superfamily / Staphylokinase/Streptokinase family / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsRao, Z. / Jiang, F. / Liu, Y. / Zhang, X. / Chen, Y. / Bartlam, M. / Song, H. / Ding, Y.
CitationJournal: To be published
Title: Crystal Structure of Staphylokinase Dimer Offers New Clue to Reduction of Immunogenicity
Authors: Rao, Z. / Jiang, F. / Liu, Y. / Zhang, X. / Chen, Y. / Bartlam, M. / Song, H. / Ding, Y.
History
DepositionFeb 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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: STAPHYLOKINASE


Theoretical massNumber of molelcules
Total (without water)15,4881
Polymers15,4881
Non-polymers00
Water28816
1
A: STAPHYLOKINASE

A: STAPHYLOKINASE


Theoretical massNumber of molelcules
Total (without water)30,9752
Polymers30,9752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_445x-1/2,y-1/2,z1
Unit cell
Length a, b, c (Å)43.92, 59.84, 102.88
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
DetailsIt is proposed in the primary citation that the biological unit is a "head-to-tail" dimer (pdb entry 1c77). Two other dimers have been considered, with alpha helices at the interface (1c78) and beta sheets at the interface (1c79) respectively. However, the "head-to-tail" dimer interface allows for the formation of strong hydrophobic interactions as well as hydrogen bonds and is more stable than the other two forms. The authors have experimental evidence from site direct mutagenesis which supports their proposition.

-
Components

#1: Protein STAPHYLOKINASE / SAK


Mass: 15487.585 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P68802, aureolysin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, pH 8.0, vapor diffusion/hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 6589 / Num. obs: 6589 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 12.8
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.182 / Num. unique all: 803 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.25→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.273 672 -
Rwork0.201 --
all0.206 6137 -
obs0.216 6400 91.3 %
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 0 16 997
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2.01

+
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