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Yorodumi- PDB-1g3k: CRYSTAL STRUCTURE OF THE H. INFLUENZAE PROTEASE HSLV AT 1.9 A RES... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g3k | ||||||
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Title | CRYSTAL STRUCTURE OF THE H. INFLUENZAE PROTEASE HSLV AT 1.9 A RESOLUTION | ||||||
Components | ATP-DEPENDENT PROTEASE HSLV | ||||||
Keywords | HYDROLASE | ||||||
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: Cell(Cambridge,Mass.) / Year: 2000 Title: Crystal and solution structures of an HslUV protease-chaperone complex. Authors: Sousa, M.C. / Trame, C.B. / Tsuruta, H. / Wilbanks, S.M. / Reddy, V.S. / McKay, D.B. | ||||||
History |
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Remark 600 | HETEROGEN HOH 201-270 IS ASSOCIATED WITH CHAIN A. HOH 1201-1269 IS ASSOCIATED WITH CHAIN B. HOH ...HETEROGEN HOH 201-270 IS ASSOCIATED WITH CHAIN A. HOH 1201-1269 IS ASSOCIATED WITH CHAIN B. HOH 2201-2260 IS ASSOCIATED WITH CHAIN C. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g3k.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g3k.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 1g3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/1g3k ftp://data.pdbj.org/pub/pdb/validation_reports/g3/1g3k | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dodecamer which can be constructed as follows: 1) Take chains A,B and C, apply symm op x,-y,-z, and translate 0 0 1 2) Finally take all six chains and apply symm op -x,-y,z |
-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) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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: 2.68 Å3/Da / Density % sol: 54.04 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Sodium Citrate, PEG 400, HCl Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 Details: This particular structure is not described in this paper. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 12, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 48317 / Num. obs: 48317 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 7.3 / Num. unique all: 4815 / % possible all: 100 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: E. Coli HslV at 3.8A Resolution: 1.9→29.34 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3798393.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.17 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→29.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.009 / 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 σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.2 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.258 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.219 |