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Yorodumi- PDB-1nqd: CRYSTAL STRUCTURE OF CLOSTRIDIUM HISTOLYTICUM COLG COLLAGENASE CO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nqd | ||||||
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Title | CRYSTAL STRUCTURE OF CLOSTRIDIUM HISTOLYTICUM COLG COLLAGENASE COLLAGEN-BINDING DOMAIN 3B AT 1.65 ANGSTROM RESOLUTION IN PRESENCE OF CALCIUM | ||||||
Components | class 1 collagenase | ||||||
Keywords | HYDROLASE / BETA SANDWICH / METALLOPROTEASE / COLLAGEN-BINDING DOMAIN / CALCIUM | ||||||
Function / homology | Function and homology information tripeptidase activity / microbial collagenase / collagen metabolic process / collagen binding / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Clostridium histolyticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Wilson, J.J. / Matsushita, O. / Okabe, A. / Sakon, J. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: A Bacterial Collagen-Binding Domain with Novel Calcium-Binding Motif Controls Domain Orientation Authors: Wilson, J.J. / Matsushita, O. / Okabe, A. / Sakon, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nqd.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nqd.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 1nqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nqd_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 1nqd_full_validation.pdf.gz | 443.5 KB | Display | |
Data in XML | 1nqd_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 1nqd_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/1nqd ftp://data.pdbj.org/pub/pdb/validation_reports/nq/1nqd | HTTPS FTP |
-Related 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: 13805.190 Da / Num. of mol.: 2 / Fragment: COLLAGEN-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium histolyticum (bacteria) / Gene: ColG / Plasmid: pGEX-4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q9S0X0, UniProt: Q9X721*PLUS, microbial collagenase #2: Chemical | ChemComp-CA / #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: 1.92 Å3/Da / Density % sol: 36 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 3350, lithium chloride, sodium acetate, glycerol, calcium nitrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X25 / Wavelength: 0.9795 / Wavelength: 0.9795 Å |
Detector | Type: BRANDEIS / Detector: CCD / Date: Oct 1, 2000 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→8 Å / Num. all: 27831 / Num. obs: 27436 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.058 / Net I/σ(I): 12.64 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.36 / Num. unique all: 2526 / Rsym value: 0.248 / % possible all: 90.9 |
Reflection | *PLUS Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS % possible obs: 90.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: APO-COLGS3B Resolution: 1.65→8 Å / Num. parameters: 8918 / Num. restraintsaints: 7758 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 18 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2119.5 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→8 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.191 | |||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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