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Yorodumi- PDB-1ht2: Nucleotide-Dependent Conformational Changes in a Protease-Associa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ht2 | ||||||
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Title | Nucleotide-Dependent Conformational Changes in a Protease-Associated ATPase HslU | ||||||
Components |
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Keywords | CHAPERONE / HSLVU / PEPTIDASE-ATPASE COMPLEX | ||||||
Function / homology | Function and homology information HslU-HslV peptidase / protein denaturation / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity / cellular response to heat ...HslU-HslV peptidase / protein denaturation / HslUV protease complex / proteasome-activating activity / proteasome core complex / protein unfolding / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity / cellular response to heat / response to heat / protein domain specific binding / magnesium ion binding / ATP hydrolysis activity / proteolysis / ATP binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Wang, J. / Song, J.J. / Seong, I.S. / Franklin, M.C. / Kamtekar, S. / Eom, S.H. / Chung, C.H. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Nucleotide-dependent conformational changes in a protease-associated ATPase HsIU. Authors: Wang, J. / Song, J.J. / Seong, I.S. / Franklin, M.C. / Kamtekar, S. / Eom, S.H. / Chung, C.H. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Mutational Studies of Hslu and its Docking Mode With Hslv. Authors: Song, H.K. / Hartmann, C. / Ramachandran, R. / Bochtler, M. / Behrendt, R. / Moroder, L. / Huber, R. #2: Journal: Nature / Year: 2000 Title: The Structures of Hslu and the ATP-Dependent Protease HslU-HslV. Authors: Bochtler, M. / Hartmann, C. / Song, H.K. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R. #3: Journal: Cell(Cambridge,Mass.) / Year: 2000 Title: Crystal and Solution Structures of an HslUV Protease-chaperone Complex. Authors: Sousa, M.C. / Trame, C.B. / Tsuruta, S. / Wilbanks, S.M. / Reddy, V.S. / McKay, D.B. #4: Journal: Structure / Year: 2001 Title: Crystal Structures of the Hslvu Peptidase-ATPase Complex Reveal an ATP-Dependent Proteolysis Mechanism Authors: Wang, J. / Song, J.J. / Franklin, M.C. / Kamtekar, S. / Im, Y.J. / Rho, S.H. / Seong, I.S. / Lee, C.S. / Chung, C.H. / Eom, S.H. #5: Journal: Nature / Year: 2000 Title: ATP-dependent proteases: Docking of Components in a Bacterial Complex Authors: Ishikawa, T. / Maurizi, M.R. / Belnap, D. / Steven, A.C. #6: Journal: J.STRUCT.BIOL. / Year: 2001 Title: A corrected quaternary arrangement of the peptidase hslv and atpase hslu in a cocrystal structure Authors: Wang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ht2.cif.gz | 575.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ht2.ent.gz | 469.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ht2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ht2_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 1ht2_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 1ht2_validation.xml.gz | 124.2 KB | Display | |
Data in CIF | 1ht2_validation.cif.gz | 164.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/1ht2 ftp://data.pdbj.org/pub/pdb/validation_reports/ht/1ht2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 18986.641 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Cellular location: CYTOPLASM / Plasmid: PET12B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A7B8 #2: Protein | Mass: 50495.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Cellular location: CYTOPLASM / Plasmid: PET12B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6H5 #3: Chemical | ChemComp-ADP / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.14 % |
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Crystal grow | *PLUS Method: unknown |
-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
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Refinement | Resolution: 2.8→29.62 Å / Data cutoff high absF: 683901.76 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 Details: THIS ENTRY CONTAINS A SOLUTION IN X-RAY STRUCTURES TO THE X-RAY DIFFRACTION DATA THAT WERE RETRIEVED FROM PDB DATABASE UNDER ACCESSION NUMBER 1E94. THIS ENTRY IS RELATED TO 1HQY, 1HT1 AND ...Details: THIS ENTRY CONTAINS A SOLUTION IN X-RAY STRUCTURES TO THE X-RAY DIFFRACTION DATA THAT WERE RETRIEVED FROM PDB DATABASE UNDER ACCESSION NUMBER 1E94. THIS ENTRY IS RELATED TO 1HQY, 1HT1 AND 1E94. THE ASSIGNMENT OF THE SCREW AXIS 6(3) IN THE P6(3)22 SPACE GROUP FOR THE HSLVU COMPLEX STRUCTURES DESCRIBED IN REFERENCES 1 AND 2 BELOW (CORRESPONDING PDB ACCESSION NUMBERS ARE 1DOO AND 1E94, RESPECTIVELY) REQUIRES THE PRESENCE OF SYSTEMATIC EXTINCTIONS ALONG (00L) WITH L=2N+1. THERE WERE NO SYSTEMATIC EXTINCTIONS AT ALL IN THE 1E94SF ENTRY. THERE WERE TWO REFLECTIONS WITH F/SIGMA(F) NEAR 20 AND NINE REFLECTIONS WITH F/SIMGA(F) OVER 10 ALONG (00L) WITH L=2N+1. SUCH A LARGE NUMBER OF SIGNIFICANT OBSERVATIONS CANNOT BE DUE TO TECHNICAL ERRORS IN MEASUREMENT OF X-RAY DIFFRACTION DATA. A STATISTICAL ANALYSIS OF THEM COMPARED WITH THE REST OF THE DATA CONFIRMS THAT THEY ARE NOT DUE TO TECHNICAL ERRORS. THEREFORE, THE SPACE GROUP MUST NOT BE P6(3)22. LARGE VALUES OF COMBINED R-MERGE VALUES FOR OBSERVED DATA 1DOO (14.1%) AND 1E94 (12.1%) ARE INDICATIVE OF INCORRECT ASSIGNEMENT OF POINT SYMMETRY GROUP TO BE 622. THE ESTIMATED MEASUREMENT PRECISION IN INTENSITY SHOULD BE ABOUT 1% ON THE BASIS OF THE AVERAGE F/SIGMA(F) OF 44.7 IN 1E94 OBSERVED DATA. THEREFORE, ONE SETS OF DYADS IN THE POINT SYMMETRY P622 WERE TWINNING OPERATIONS. THERE WERE LARGE DISCREPANCIES IN WILSON RATIO (/^2) BETWEEN THE OBSERVED DATA AND CALCULATED DATA FROM THE COORDINATE 1E94 IN THE FOLLOWING ZONES: L=2N, L=2N+1, H+K=3N/L=2N; H+K != 3N/L=2N, AND ALL HKL. SOME WERE LARGE THAN 70% AND SOME WERE AS SMALL AS 5%. THIS SUGGESTS THAT X-RAY DATA WERE PROCESSED FROM TWINNED CRYSTALS. THERE WERE ALSO LARGE DIFFERENCES IN THE FIRST AND SECOND MOMENTS OF THE DIFFERENCES (FOBS-FCALC). THIS IS ANOTHER STATISTICAL INDICATOR FOR THE TWINNING PROBLEM. THE CORRECT POINT GROUP OF 1E94 SHOULD BE LOWER THAN P622, BECAUSE OF LARGE RMERGE VALUES AS INDICATIVE OF NON 50%:50% TWINNING. THE CORRECT SPACE GROUP SHOULD BE EITHER P321 OR P312. THE SPACE GROUP SHOULD ONLY BE DETERMINED FROM THE ORIGINAL INTEGRATED DATA BEFORE SCALING, SO SHOULD BE THE CORRECT TWINNING FRACTION. WITHOUT THE ORIGINAL DATA, THE TWINNING FRACTION COULD ONLY BE TREATED AS 50%:50% AND THE SPACE GROUP SHOULD BE CONSIDERED TO BE EITHER P312 (THIS ENTRY) OR P321 (ENTRY 1HT1). THE DATA TO THE LOWER SPACE GROUP WERE EXPANDED BY THE (-H,-K,L) OPERATION. THE STRUCTURE FACTOR FILE WAS TAKEN FROM 1E94 AND EXPANDED BY THE (-H,-K,L) OPERATION WITH FREE R-FACTOR SELECTION INCLUDED.
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Refinement step | Cycle: LAST / Resolution: 2.8→29.62 Å
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Xplor file |
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