[English] 日本語
Yorodumi
- PDB-1mbx: CRYSTAL STRUCTURE ANALYSIS OF ClpSN WITH TRANSITION METAL ION BOUND -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mbx
TitleCRYSTAL STRUCTURE ANALYSIS OF ClpSN WITH TRANSITION METAL ION BOUND
Components
  • ATP-Dependent clp Protease ATP-Binding Subunit clp A
  • Protein yljA
KeywordsPROTEIN BINDING / Adaptors / Hsp100/Clp chaperone / AAA+ family / ATP-dependent protease
Function / homology
Function and homology information


endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / molecular function inhibitor activity / protein unfolding / protein catabolic process / cellular response to heat / response to heat / protein-folding chaperone binding / response to oxidative stress ...endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / molecular function inhibitor activity / protein unfolding / protein catabolic process / cellular response to heat / response to heat / protein-folding chaperone binding / response to oxidative stress / ATP hydrolysis activity / proteolysis / ATP binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS / ATP-dependent Clp protease adaptor protein ClpS / Double Clp-N motif / Clp, N-terminal domain / ATP-dependent Clp protease ATP-binding subunit ClpA / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Ribosomal Protein L30; Chain: A, / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. ...Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS / ATP-dependent Clp protease adaptor protein ClpS / Double Clp-N motif / Clp, N-terminal domain / ATP-dependent Clp protease ATP-binding subunit ClpA / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Ribosomal Protein L30; Chain: A, / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-YBT / ATP-dependent Clp protease adapter protein ClpS / ATP-dependent Clp protease ATP-binding subunit ClpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGuo, F. / Esser, L. / Singh, S.K. / Maurizi, M.R. / Xia, D.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of the Heterodimeric Complex of the Adaptor, ClpS, with the N-domain of the AAA+ Chaperone, ClpA
Authors: Guo, F. / Esser, L. / Singh, S.K. / Maurizi, M.R. / Xia, D.
History
DepositionAug 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-Dependent clp Protease ATP-Binding Subunit clp A
B: ATP-Dependent clp Protease ATP-Binding Subunit clp A
C: Protein yljA
D: Protein yljA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,40615
Polymers56,4724
Non-polymers1,93311
Water3,315184
1
A: ATP-Dependent clp Protease ATP-Binding Subunit clp A
C: Protein yljA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9906
Polymers28,2362
Non-polymers7544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-53 kcal/mol
Surface area12620 Å2
MethodPISA
2
B: ATP-Dependent clp Protease ATP-Binding Subunit clp A
D: Protein yljA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4169
Polymers28,2362
Non-polymers1,1797
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-66 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.436, 87.436, 212.955
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe asymmetric unit contains two heterodimers of ClpSN

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein ATP-Dependent clp Protease ATP-Binding Subunit clp A


Mass: 16043.073 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBAD33-yljA / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 alpha / References: UniProt: P0ABH9
#2: Protein Protein yljA


Mass: 12193.038 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pFG42 / Production host: Escherichia coli (E. coli) / Strain (production host): SG22176 / References: UniProt: P0A8Q6

-
Non-polymers , 5 types, 195 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-YBT / BIS-(2-HYDROXYETHYL)AMINO-TRIS(HYDROXYMETHYL)METHANE YTTRIUM


Mass: 298.146 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H19NO5Y
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: glycerol, bis-tris , yttrium chloride, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Mbis-Tris1reservoirpH6.5
232 %glycerol1reservoir
310-15 mMyttrium chloride1reservoir
410 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 26, 2002 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 48936 / Num. obs: 48936 / % possible obs: 92.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 39.2 Å2 / Rsym value: 0.046 / Net I/σ(I): 46.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 2313 / Rsym value: 0.679 / % possible all: 48.4
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 50 Å / Num. obs: 45812 / % possible obs: 95.9 % / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 69.9 % / Rmerge(I) obs: 0.638

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MBU

1mbu


Resolution: 2.25→19.54 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 511609.52 / Data cutoff high rms absF: 511609.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4404 10 %RANDOM
Rwork0.208 ---
all-43733 --
obs-43733 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.8654 Å2 / ksol: 0.347116 e/Å3
Displacement parametersBiso mean: 48.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å21.99 Å20 Å2
2---1.84 Å20 Å2
3---3.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3631 0 96 184 3911
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.592
X-RAY DIFFRACTIONc_scangle_it3.792.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 569 9.3 %
Rwork0.354 9247 -
obs-5631 71 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3YBT.PARYBT.TOP
X-RAY DIFFRACTION4GOL.PARGOL.TOP
X-RAY DIFFRACTION5ION.PARION.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0116
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08
LS refinement shell
*PLUS
Rfactor Rfree: 0.354 / Rfactor Rwork: 0.351

+
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