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Yorodumi- PDB-1jjw: Structure of Haemophilus influenzae HslV Protein at 1.9 A Resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jjw | ||||||
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Title | Structure of Haemophilus influenzae HslV Protein at 1.9 A Resolution | ||||||
Components | ATP-DEPENDENT PROTEASE HSLV | ||||||
Keywords | HYDROLASE / K anomalous scattering / quasi-equivalent packing | ||||||
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 | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sousa, M.C. / McKay, D.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structure of Haemophilus influenzae HslV protein at 1.9 A resolution, revealing a cation-binding site near the catalytic site. Authors: Sousa, M.C. / McKay, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jjw.cif.gz | 110.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jjw.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/1jjw ftp://data.pdbj.org/pub/pdb/validation_reports/jj/1jjw | HTTPS FTP |
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-Related structure data
Related structure data | 1g3kS 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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-Components
#1: Protein | Mass: 18903.549 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HslV / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P43772, EC: 3.4.99.- #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: 2.69 Å3/Da / Density % sol: 54.21 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: sodium citrate, HCl Tris, PEG 400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL9-2 / Wavelength: 1.55 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 6, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.55 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 46472 / Num. obs: 46472 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 9.1 / Rsym value: 0.195 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G3K Resolution: 1.9→19.9 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3273928.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.2708 Å2 / ksol: 0.36033 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 33.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 9.8 % / Rfactor obs: 0.217 / Rfactor Rfree: 0.251 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.7 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.97 Å / Rfactor Rfree: 0.334 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.254 / Rfactor obs: 0.258 |