+Open data
-Basic information
Entry | Database: PDB / ID: 1m4y | ||||||
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Title | Crystal structure of HslV from Thermotoga maritima | ||||||
Components | ATP-dependent protease hslV | ||||||
Keywords | HYDROLASE / N-terminal catalytic Threonine residue | ||||||
Function / homology | Function and homology information HslU-HslV peptidase / HslUV protease complex / proteasome core complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Song, H.K. / Ramachandran, R. / Bochtler, M.B. / Hartmann, C. / Azim, M.K. / Huber, R. | ||||||
Citation | Journal: BIOPHYS.CHEM. / Year: 2003 Title: Isolation and characterization of the prokaryotic proteasome homolog HslVU (ClpQY) from Thermotoga maritima and the crystal structure of HslV. Authors: Song, H.K. / Bochtler, M. / Azim, M.K. / Hartmann, C. / Huber, R. / Ramachandran, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m4y.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m4y.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 1m4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m4y_validation.pdf.gz | 438.7 KB | Display | wwPDB validaton report |
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Full document | 1m4y_full_validation.pdf.gz | 442.9 KB | Display | |
Data in XML | 1m4y_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 1m4y_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/1m4y ftp://data.pdbj.org/pub/pdb/validation_reports/m4/1m4y | HTTPS FTP |
-Related structure data
Related structure data | |
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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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-Components
#1: Protein | Mass: 18354.037 Da / Num. of mol.: 3 / Fragment: Three protomers Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: Q9WYZ1, Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases #2: Chemical | #3: 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: 2.41 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MPD, magnesium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 15, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 31188 / % possible obs: 99.3 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.1→2.14 Å / % possible all: 99.7 |
Reflection | *PLUS Lowest resolution: 17 Å / Redundancy: 10.7 % / Num. measured all: 334480 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.249 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.14 Å / Rfactor Rfree error: 0.012
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Refinement | *PLUS Lowest resolution: 17 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.191 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.24 |