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- PDB-2xsm: Crystal structure of the mammalian cytosolic chaperonin CCT in co... -

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Basic information

Entry
Database: PDB / ID: 2xsm
TitleCrystal structure of the mammalian cytosolic chaperonin CCT in complex with tubulin
Components(CCT) x 15
KeywordsCHAPERONE / CHAPERONINE GROUP II
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 5.5 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, H, I, J, K, L, O, M, N, P
AuthorsMunoz, I.G. / Yebenes, H. / Zhou, M. / Mesa, P. / Serna, M. / Bragado-Nilsson, E. / Beloso, A. / Robinson, C.V. / Valpuesta, J.M. / Montoya, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Crystal Structure of the Open Conformation of the Mammalian Chaperonin Cct in Complex with Tubulin.
Authors: Munoz, I.G. / Yebenes, H. / Zhou, M. / Mesa, P. / Serna, M. / Park, A.Y. / Bragado-Nilsson, E. / Beloso, A. / De Carcer, G. / Malumbres, M. / Robinson, C.V. / Valpuesta, J.M. / Montoya, G.
History
DepositionOct 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCT
B: CCT
C: CCT
D: CCT
E: CCT
F: CCT
G: CCT
H: CCT
I: CCT
J: CCT
K: CCT
L: CCT
M: CCT
N: CCT
O: CCT
P: CCT


Theoretical massNumber of molelcules
Total (without water)548,19316
Polymers548,19316
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)272.700, 313.500, 158.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 15 types, 16 molecules ABCDEFGHIJKLOMNP

#1: Protein CCT / Coordinate model: Cα atoms only


Mass: 41634.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES / Tissue: TESTES
#2: Protein CCT / Coordinate model: Cα atoms only


Mass: 40698.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES
#3: Protein CCT / Coordinate model: Cα atoms only


Mass: 38740.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES
#4: Protein CCT / Coordinate model: Cα atoms only


Mass: 40102.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES
#5: Protein CCT / Coordinate model: Cα atoms only


Mass: 40187.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES
#6: Protein CCT / Coordinate model: Cα atoms only


Mass: 39676.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES
#7: Protein CCT / Coordinate model: Cα atoms only


Mass: 41293.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES
#8: Protein CCT / Coordinate model: Cα atoms only


Mass: 40357.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES
#9: Protein CCT / Coordinate model: Cα atoms only


Mass: 24953.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES
#10: Protein CCT / Coordinate model: Cα atoms only


Mass: 25464.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES
#11: Protein CCT


Mass: 33549.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES
#12: Protein CCT / Coordinate model: Cα atoms only


Mass: 25294.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES
#13: Protein CCT / Coordinate model: Cα atoms only


Mass: 25379.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES
#14: Protein CCT / Coordinate model: Cα atoms only


Mass: 24613.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES
#15: Protein CCT / Coordinate model: Cα atoms only


Mass: 40953.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TESTES FROM BULLS OBTAINED FROM A SLAUGHTERHOUSE / Source: (natural) BOS TAURUS (domestic cattle) / Organ: TESTES

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 60 %
Description: THE STRUCTURE WAS SOLVED BY SAD. TWO DATA SETS WERE COLLECTED AT THE PEAK, 1.2548A, AND INFLECTION, 1.114A POINTS FOR TAMTALUM USING A CRYSTAL DERIVATIZED WITH TABR. FOUR TAMTALUM SITES ...Description: THE STRUCTURE WAS SOLVED BY SAD. TWO DATA SETS WERE COLLECTED AT THE PEAK, 1.2548A, AND INFLECTION, 1.114A POINTS FOR TAMTALUM USING A CRYSTAL DERIVATIZED WITH TABR. FOUR TAMTALUM SITES WERE IDENTIFIED AND INITIAL PHASES CALCULATED. THE FINAL MODEL WAS BUILT AFTER PHASE EXTENSION USING A NATIVE DATA SET AT 5.5A RESOLUTION.
Crystal growpH: 6
Details: 1 M LICL, 100 MM MES PH 6, 10% PEG6000, 10% OF THE OPTIC SALT SUITE NUMBER 63 FROM QIAGEN, AND 5% OF TERT-BUTANOL FROM HAMPTON RESEARCH ADDITIVE SCREEN.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.114
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.114 Å / Relative weight: 1
ReflectionResolution: 5.5→100 Å / Num. obs: 74325 / % possible obs: 92.5 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.54
Reflection shellResolution: 5.5→6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.2 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0099refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 5.5→100 Å / Num. reflection obs: 45495 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE MODEL WAS DONE USING A CALPHA TRACE FROM THE THERMOSOME STRUCTURE, PDB ENTRY 1GN1. THE CCT MODEL CONTAINS THE 16 EQUATORIAL DOMAINS, 16 INTERMEDIATE DOMAINS AND 10 OUT OF 16 APICAL DOMAINS
Refinement stepCycle: LAST / Resolution: 5.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6438 0 0 0 6438

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