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Yorodumi- PDB-2c8t: The 3.0 A Resolution Structure of Caseinolytic Clp Protease 1 fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c8t | ||||||
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Title | The 3.0 A Resolution Structure of Caseinolytic Clp Protease 1 from Mycobacterium tuberculosis | ||||||
Components | ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1 | ||||||
Keywords | HYDROLASE / SERINE PROTEASE / CLPP1 | ||||||
Function / homology | Function and homology information endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ingvarsson, H. / Hogbom, M. / Jones, T.A. / Unge, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Insights Into the Inter-Ring Plasticity of Caseinolytic Proteases from the X-Ray Structure of Mycobacterium Tuberculosis Clpp1. Authors: Ingvarsson, H. / Mate, M.J. / Hogbom, M. / Portnoi, D. / Benaroudj, N. / Alzari, P.M. / Ortiz-Lombardia, M. / Unge, T. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c8t.cif.gz | 437.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c8t.ent.gz | 362.1 KB | Display | PDB format |
PDBx/mmJSON format | 2c8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c8t_validation.pdf.gz | 547.6 KB | Display | wwPDB validaton report |
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Full document | 2c8t_full_validation.pdf.gz | 596.9 KB | Display | |
Data in XML | 2c8t_validation.xml.gz | 79.9 KB | Display | |
Data in CIF | 2c8t_validation.cif.gz | 105.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/2c8t ftp://data.pdbj.org/pub/pdb/validation_reports/c8/2c8t | HTTPS FTP |
-Related structure data
Related structure data | 2cbyC 2ce3C 1tyfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 22408.385 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET101D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A526, UniProt: P9WPC5*PLUS, endopeptidase Clp |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.21 % |
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Crystal grow | pH: 5.2 Details: 5 MG/ML PROTEIN, 100 MM TRI-NA-CITRATE, PH 5.2, 3% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 7, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 3→59.4 Å / Num. obs: 60193 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 3→3.16 Å / Rmerge(I) obs: 0.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TYF Resolution: 3→19.87 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.894 / SU B: 39.873 / SU ML: 0.323 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.94 Å2
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Refinement step | Cycle: LAST / Resolution: 3→19.87 Å
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Refine LS restraints |
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