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Yorodumi- PDB-1wme: Crystal Structure of alkaline serine protease KP-43 from Bacillus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wme | ||||||
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Title | Crystal Structure of alkaline serine protease KP-43 from Bacillus sp. KSM-KP43 (1.50 angstrom, 293 K) | ||||||
Components | protease | ||||||
Keywords | HYDROLASE / alpha-beta hydrolase fold / jelly-roll beta-barrel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å | ||||||
Authors | Nonaka, T. / Fujihashi, M. / Kita, A. / Saeki, K. / Ito, S. / Horikoshi, K. / Miki, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The Crystal Structure of an Oxidatively Stable Subtilisin-like Alkaline Serine Protease, KP-43, with a C-terminal {beta}-Barrel Domain Authors: Nonaka, T. / Fujihashi, M. / Kita, A. / Saeki, K. / Ito, S. / Horikoshi, K. / Miki, K. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and preliminary X-ray diffraction studies of a novel alkaline serine protease (KP-43) from alkaliphilic Bacillus sp. strain KSM-KP43 Authors: Nonaka, T. / Fujihashi, M. / Kita, A. / Saeki, K. / Ito, S. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wme.cif.gz | 182.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wme.ent.gz | 145.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wme_validation.pdf.gz | 420.1 KB | Display | wwPDB validaton report |
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Full document | 1wme_full_validation.pdf.gz | 422.5 KB | Display | |
Data in XML | 1wme_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 1wme_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/1wme ftp://data.pdbj.org/pub/pdb/validation_reports/wm/1wme | HTTPS FTP |
-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 monomer. |
-Components
#1: Protein | Mass: 45338.840 Da / Num. of mol.: 1 / Fragment: residues 1-434 / Source method: isolated from a natural source / Source: (natural) Bacillus sp. (bacteria) / Strain: KSM-KP43 References: UniProt: Q93UV9, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 0.1M HEPES-NaOH pH 7.3, 1.7M ammonium sulfate, 10mM calcium chloride, 10% (v/v) 1,4-dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUAMTUM 4r / Detector: CCD / Date: Oct 29, 2000 / Details: bent plane mirror of fused quartz |
Radiation | Monochromator: silicon (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→100 Å / Num. obs: 63023 / % possible obs: 96 % / Redundancy: 4.063 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.712 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 3.041 / % possible all: 59.2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.5→26 Å / Num. parameters: 31201 / Num. restraintsaints: 39646 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Water molecules from HOH 2208 to 2211 are related to multi-conformational ASN A 1.
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Refine analyze | Num. disordered residues: 17 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3375.4 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→26 Å
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Refine LS restraints |
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