[English] 日本語
Yorodumi
- PDB-1tyf: THE STRUCTURE OF CLPP AT 2.3 ANGSTROM RESOLUTION SUGGESTS A MODEL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tyf
TitleTHE STRUCTURE OF CLPP AT 2.3 ANGSTROM RESOLUTION SUGGESTS A MODEL FOR ATP-DEPENDENT PROTEOLYSIS
ComponentsCLP PEPTIDASE
KeywordsPEPTIDASE
Function / homology
Function and homology information


HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteasomal protein catabolic process / serine-type peptidase activity / response to radiation ...HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteasomal protein catabolic process / serine-type peptidase activity / response to radiation / ATPase binding / response to heat / serine-type endopeptidase activity / proteolysis / identical protein binding / membrane / cytosol
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsWang, J. / Hartling, J.A. / Flanagan, J.M.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: The structure of ClpP at 2.3 A resolution suggests a model for ATP-dependent proteolysis.
Authors: Wang, J. / Hartling, J.A. / Flanagan, J.M.
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Sequence and Structure of Clp P, the Proteolytic Component of the ATP-Dependent Clp Protease of Escherichia Coli
Authors: Maurizi, M.R. / Clark, W.P. / Katayama, Y. / Rudikoff, S. / Pumphrey, J. / Bowers, B. / Gottesman, S.
History
DepositionOct 13, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CLP PEPTIDASE
B: CLP PEPTIDASE
C: CLP PEPTIDASE
D: CLP PEPTIDASE
E: CLP PEPTIDASE
F: CLP PEPTIDASE
G: CLP PEPTIDASE
H: CLP PEPTIDASE
I: CLP PEPTIDASE
J: CLP PEPTIDASE
K: CLP PEPTIDASE
L: CLP PEPTIDASE
M: CLP PEPTIDASE
N: CLP PEPTIDASE


Theoretical massNumber of molelcules
Total (without water)302,21614
Polymers302,21614
Non-polymers00
Water22,4471246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57940 Å2
ΔGint-212 kcal/mol
Surface area89880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.320, 102.460, 157.080
Angle α, β, γ (deg.)90.00, 97.80, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
CLP PEPTIDASE / CLPP


Mass: 21586.863 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A6G7, endopeptidase Clp
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1246 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 55 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110.4 mg/mlprotein1drop
210 mMHEPES1drop
3200 mM1dropNaCl
41 mMdithiothreitol1drop
5100 mMNa citrate1reservoir
610 %(w/v)PEG40001reservoir
720 %(v/v)isopropanol1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
DetectorDetector: CCD / Date: Dec 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection% possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.077
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 80 Å / Num. obs: 142952

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
HKL(DENZO)data reduction
HKL(SCALEPACK)data scaling
X-PLORphasing
RefinementResolution: 2.3→80 Å / σ(F): 2
RfactorNum. reflection
Rfree0.292 -
Rwork0.219 -
obs0.219 131572
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20062 0 0 1246 21308
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.53
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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