[English] 日本語
Yorodumi
- PDB-1ass: APICAL DOMAIN OF THE CHAPERONIN FROM THERMOPLASMA ACIDOPHILUM -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1ass
TitleAPICAL DOMAIN OF THE CHAPERONIN FROM THERMOPLASMA ACIDOPHILUM
ComponentsTHERMOSOME
KeywordsCHAPERONIN / HSP60 / THERMOSOME / TCP1 / GROEL / THERMOPLASMA ACIDOPHILUM / ATP-BINDING
Function / homologyChaperonin TCP-1, conserved site / Chaperonin Cpn60/TCP-1 family / Thermosome, archaeal / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like apical domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like equatorial domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. ...Chaperonin TCP-1, conserved site / Chaperonin Cpn60/TCP-1 family / Thermosome, archaeal / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like apical domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like equatorial domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonins TCP-1 signature 3. / protein folding / unfolded protein binding / ATP binding / Thermosome subunit alpha
Function and homology information
Specimen sourceThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / 2.3 Å resolution
AuthorsKlumpp, M. / Baumeister, W. / Essen, L.-O.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1997
Title: Structure of the substrate binding domain of the thermosome, an archaeal group II chaperonin.
Authors: Klumpp, M. / Baumeister, W. / Essen, L.O.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 11, 1997 / Release: Dec 3, 1997
RevisionDateData content typeGroupProviderType
1.0Dec 3, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THERMOSOME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1315
Polyers17,8231
Non-polymers3084
Water63135
1
A: THERMOSOME
hetero molecules

A: THERMOSOME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,26110
Polyers35,6452
Non-polymers6168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area (Å2)3910
ΔGint (kcal/M)-75
Surface area (Å2)14710
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)82.350, 82.350, 77.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP 31 2 1

-
Components

#1: Protein/peptide THERMOSOME /


Mass: 17822.625 Da / Num. of mol.: 1
Fragment: ALPHA-SUBUNIT, APICAL DOMAIN, SUBSTRATE-BINDING DOMAIN
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Genus: Thermoplasma / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: THSA / Plasmid name: PRSET6A / Genus (production host): Escherichia / Species (production host): Escherichia coli / Gene (production host): THSA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P48424
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Formula: PO4 / Phosphate
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.27 / Density percent sol: 7 %
Crystal growpH: 3.5 / Details: pH 3.5
Crystal grow
*PLUS
Temp: 30 ℃ / pH: 3.8 / Method: vapor diffusion
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
127 mg/mlprotein1drop
23.0 Mammonium sulfate1drop
30.1 Msodium citrate1drop

-
Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Apr 14, 1997
RadiationMonochromator: SI(111) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 57.4 Å2 / D resolution high: 2.3 Å / D resolution low: 18 Å / Number obs: 10935 / Observed criterion sigma I: -3 / Rmerge I obs: 0.05 / NetI over sigmaI: 24.3 / Redundancy: 4 % / Percent possible obs: 96.3
Reflection shellRmerge I obs: 0.256 / Highest resolution: 2.3 Å / MeanI over sigI obs: 7 / Percent possible all: 95.5
Reflection
*PLUS
Number measured all: 44064
Reflection shell
*PLUS
Percent possible obs: 95.5

-
Processing

Software
NameVersionClassification
MLPHAREphasing
SOLOMONphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MIR / R Free selection details: CONCENTRIC SHELLS / Data cutoff high absF: 1 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: RFREE / Sigma F: 0
Displacement parametersB iso mean: 6 Å2 / Aniso B11: 22.95 Å2 / Aniso B12: 8.95 Å2 / Aniso B13: 0 Å2 / Aniso B22: 22.95 Å2 / Aniso B23: 0 Å2 / Aniso B33: 16.28 Å2
Least-squares processR factor R free: 0.251 / R factor R work: 0.222 / R factor obs: 0.222 / Highest resolution: 2.3 Å / Lowest resolution: 1 Å / Number reflection R free: 516 / Number reflection obs: 12774 / Percent reflection R free: 4 / Percent reflection obs: 96.3
Refine analyzeLuzzati coordinate error free: 0.48 Å / Luzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.43 Å / Luzzati sigma a obs: 0.46 Å
Refine hist #LASTHighest resolution: 2.3 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 1175 / Nucleic acid: 0 / Ligand: 16 / Solvent: 35 / Total: 1226
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
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_deg2.031
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.70
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.686
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.251.50
X-RAY DIFFRACTIONx_mcangle_it4.622.00
X-RAY DIFFRACTIONx_scbond_it5.062.00
X-RAY DIFFRACTIONx_scangle_it7.352.50
Refine LS shellHighest resolution: 2.33 Å / Lowest resolution: 2.4 Å / Percent reflection obs: 95.5
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.704
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.686

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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