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Yorodumi- PDB-2ce3: CRYSTAL STRUCTURE OF THE ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ce3 | ||||||
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Title | CRYSTAL STRUCTURE OF THE ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1 (CLPP1) FROM MYCOBACTERIUM TUBERCULOSIS | ||||||
Components | ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1 | ||||||
Keywords | HYDROLASE / SERINE PROTEASE / CLP PROTEASE / PROTEOLYTIC SUBUNIT / ENDOPEPTIDASE / MYCOBACTERIUM TUBERCULOSIS / ATP-DEPENDENT PROTEASE | ||||||
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: 2.6 Å | ||||||
Authors | Segelke, B. / Kim, C.Y. / Ortiz-Lombardia, M. / Alzari, P.M. / Lekin, 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 | 2ce3.cif.gz | 439.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ce3.ent.gz | 361.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ce3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ce3_validation.pdf.gz | 518.4 KB | Display | wwPDB validaton report |
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Full document | 2ce3_full_validation.pdf.gz | 554.6 KB | Display | |
Data in XML | 2ce3_validation.xml.gz | 76.9 KB | Display | |
Data in CIF | 2ce3_validation.cif.gz | 105 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/2ce3 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/2ce3 | HTTPS FTP |
-Related structure data
Related structure data | 2c8tC 2cbySC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | CLPP ENDOPEPTIDASES ARE KNOWN TO BE TETRADECAMERICAND THIS IS THE MULTIMERIC STATE FOUND IN THISSTRUCTURE.HOWEVER, IN THIS PROTEIN, GEL FILTRATION AND INTER-COMPLEX REGIONS BETWEEN THE TWO HEPTAMERIC RINGS WOULDINDICATE THAT THE OLIGOMER IS LIKELY TO BE HEPTAMERICIN SOLUTION. |
-Components
#1: Protein | Mass: 21727.664 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Description: INSTITUT PASTEUR COLLECTION / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P0A526, UniProt: P9WPC5*PLUS, endopeptidase Clp #2: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 47 % Description: STRUCTURE DETERMINED FROM COORDINATES OF SAME PROTEIN IN A DIFFERENT SPACE GROUP AT LOWER RESOLUTION |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: THE PROTEIN WAS CRYSTALLIZED BY THE SITTING DROP METHOD WITH 400NL PROTEIN PLUS 400NL MOTHERLIQUOR AND 100UL RESERVOIR. CONDITION WAS IDENTIFIED USING A SET OF RANDOM CONDITIONS GENERATED ...Details: THE PROTEIN WAS CRYSTALLIZED BY THE SITTING DROP METHOD WITH 400NL PROTEIN PLUS 400NL MOTHERLIQUOR AND 100UL RESERVOIR. CONDITION WAS IDENTIFIED USING A SET OF RANDOM CONDITIONS GENERATED WITH CRYSTOOL SOFTWARE AND OPTIMIZED TO 9.576% (W/V) PEG 2000 0.2M LITHIUM SULFATE 0.1M MOPS (4-MORPHOLINEPROPANESULFONIC ACID) PH 6.5 WITH CRYSTOOL BY REDUCING THE PARAMETER SPACE TO THE REAGENTS UTILIZED. CRYSTALS SHOWED AFTER 2 DAYS |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→49.5 Å / Num. obs: 90593 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 61.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CBY Resolution: 2.6→169.03 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / SU B: 26.043 / SU ML: 0.255 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.637 / ESU R Free: 0.322 / 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 / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→169.03 Å
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Refine LS restraints |
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