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Yorodumi- PDB-2xsm: Crystal structure of the mammalian cytosolic chaperonin CCT in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xsm | ||||||
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Title | Crystal structure of the mammalian cytosolic chaperonin CCT in complex with tubulin | ||||||
Components | (CCT) x 15 | ||||||
Keywords | CHAPERONE / CHAPERONINE GROUP II | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 5.5 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, H, I, J, K, L, O, M, N, P | ||||||
Authors | Munoz, I.G. / Yebenes, H. / Zhou, M. / Mesa, P. / Serna, M. / Bragado-Nilsson, E. / Beloso, A. / Robinson, C.V. / Valpuesta, J.M. / Montoya, G. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xsm.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xsm.ent.gz | 124.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/2xsm ftp://data.pdbj.org/pub/pdb/validation_reports/xs/2xsm | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 15 types, 16 molecules ABCDEFGHIJKLOMNP
#1: Protein | 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 (cattle) / Organ: TESTES / Tissue: TESTES | ||||||
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#2: Protein | 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 (cattle) / Organ: TESTES | ||||||
#3: Protein | 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 (cattle) / Organ: TESTES | ||||||
#4: Protein | 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 (cattle) / Organ: TESTES | ||||||
#5: Protein | 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 (cattle) / Organ: TESTES | ||||||
#6: Protein | 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 (cattle) / Organ: TESTES | ||||||
#7: Protein | 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 (cattle) / Organ: TESTES | ||||||
#8: Protein | 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 (cattle) / Organ: TESTES | ||||||
#9: Protein | 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 (cattle) / Organ: TESTES | ||||||
#10: Protein | 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 (cattle) / Organ: TESTES | ||||||
#11: Protein | 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 (cattle) / Organ: TESTES | ||||||
#12: Protein | 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 (cattle) / Organ: TESTES #13: Protein | | 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 (cattle) / Organ: TESTES #14: Protein | | 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 (cattle) / Organ: TESTES #15: Protein | | 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 (cattle) / Organ: TESTES |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density 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. |
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Crystal grow | pH: 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. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.114 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.114 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 5.5→6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.2 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method 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 step | Cycle: LAST / Resolution: 5.5→100 Å
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