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Yorodumi- PDB-1mtp: The X-ray crystal structure of a serpin from a thermophilic prokaryote -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mtp | ||||||
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Title | The X-ray crystal structure of a serpin from a thermophilic prokaryote | ||||||
Components |
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Keywords | STRUCTURAL GENOMICS / protease inhibitor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermobifida fusca (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Irving, J.A. / Cabrita, L.D. / Rossjohn, J. / Pike, R.N. / Bottomley, S.P. / Whisstock, J.C. | ||||||
Citation | Journal: Structure / Year: 2003 Title: The 1.5 A crystal structure of a prokaryote serpin: controlling conformational change in a heated environment Authors: Irving, J.A. / Cabrita, L.D. / Rossjohn, J. / Pike, R.N. / Bottomley, S.P. / Whisstock, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mtp.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mtp.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mtp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mtp_validation.pdf.gz | 370.7 KB | Display | wwPDB validaton report |
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Full document | 1mtp_full_validation.pdf.gz | 372.4 KB | Display | |
Data in XML | 1mtp_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1mtp_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/1mtp ftp://data.pdbj.org/pub/pdb/validation_reports/mt/1mtp | HTTPS FTP |
-Related structure data
Related structure data | 1hleS 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: 34976.918 Da / Num. of mol.: 1 / Fragment: Chain A, residue 55-377 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida fusca (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 23019748, UniProt: Q47NK3*PLUS |
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#2: Protein/peptide | Mass: 4787.580 Da / Num. of mol.: 1 / Fragment: Chain B, residue 378-420 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida fusca (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 23019748, UniProt: Q47NK3*PLUS |
#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: 2.16 Å3/Da / Density % sol: 42.94 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 4000, 0.1 M Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 9 / PH range high: 8 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 14, 2002 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 179258 / Num. obs: 179258 / Observed criterion σ(I): 0 |
Reflection | *PLUS Num. obs: 54979 / % possible obs: 98.1 % / Redundancy: 3.3 % / Num. measured all: 179258 / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS % possible obs: 92 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HLE Resolution: 1.5→50 Å
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 3 % | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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