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Open data
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Basic information
Entry | Database: PDB / ID: 1c7k | ||||||
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Title | CRYSTAL STRUCTURE OF THE ZINC PROTEASE | ||||||
![]() | ZINC ENDOPROTEASE | ||||||
![]() | HYDROLASE / alpha and beta protein / METALLOPROTEINASE | ||||||
Function / homology | ![]() snapalysin / metalloendopeptidase activity / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Kurisu, G. / Harada, S. / Kai, Y. | ||||||
![]() | ![]() Title: Structure of the zinc-binding site in the crystal structure of a zinc endoprotease from Streptomyces caespitosus at 1 A resolution. Authors: Kurisu, G. / Kai, Y. / Harada, S. #1: ![]() Title: Structure of the Zinc Endoprotease from Streptomyces caespitosus Authors: Kurisu, G. / Kinoshita, T. / Sugimoto, A. / Nagara, A. / Kai, Y. / Kasai, N. / Harada, S. #2: ![]() Title: Complete Amino Acid Sequence of a Zinc Metalloendoprotease from Streptomyces caespitosus Authors: Harada, S. / Kinoshita, T. / Kasai, N. / Tsunasawa, S. / Sakiyama, F. #3: ![]() Title: Crystallization and Main-Chain Structure of Neutral Protease from Streptomyces caespitosus Authors: Harada, S. / Kitadokoro, K. / Kinoshita, T. / Kai, Y. / Kasai, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.6 KB | Display | ![]() |
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PDB format | ![]() | 48.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 404.4 KB | Display | ![]() |
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Full document | ![]() | 405.5 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14387.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P56406, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1 Å3/Da / Density % sol: 37.48 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: liquid diffusion / pH: 7 Details: acetone, pH 7.0, LIQUID DIFFUSION, temperature 277K | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 35 % | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: batch method / Details: Harada, S., (1991) J.BIOCHEM.(TOKYO), 110, 46. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 18, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7107 Å / Relative weight: 1 |
Reflection | Resolution: 0.92→55 Å / Num. all: 59541 / Num. obs: 59541 / % possible obs: 81.9 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.64 |
Reflection shell | Resolution: 0.92→0.97 Å / % possible all: 58.3 |
Reflection | *PLUS Num. obs: 51419 / % possible obs: 82 % / Redundancy: 58.3 % / Num. measured all: 158614 |
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Processing
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Refinement | Method to determine structure: AB INITIO / Resolution: 1→55 Å / Num. parameters: 992 / Num. restraintsaints: 1187 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1133 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→55 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 51419 / Rfactor Rfree: 0.17 / Rfactor Rwork: 0.15 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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