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Yorodumi- PDB-1qqy: X-RAY CRYSTAL STRUCTURE ANALYSIS OF CANINE MILK LYSOZYME (APO-TYPE) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qqy | ||||||
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Title | X-RAY CRYSTAL STRUCTURE ANALYSIS OF CANINE MILK LYSOZYME (APO-TYPE) | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / APO-TYPE PROTEIN / CALCIUM BINDING LYSOZYME / ENZYME | ||||||
Function / homology | Function and homology information lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / metal ion binding Similarity search - Function | ||||||
Biological species | Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Koshiba, T. / Yao, M. / Tanaka, I. / Nitta, K. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Structure and thermodynamics of the extraordinarily stable molten globule state of canine milk lysozyme. Authors: Koshiba, T. / Yao, M. / Kobashigawa, Y. / Demura, M. / Nakagawa, A. / Tanaka, I. / Kuwajima, K. / Nitta, K. #1: Journal: Protein Eng. / Year: 1999 Title: Expression of a synthetic gene encoding canine milk lysozyme in Escherichia coli and characterization of the expressed protein Authors: Koshiba, T. / Hayashi, T. / Miwako, I. / Kumagai, I. / Ikura, T. / Kawano, K. / Nitta, K. / Kuwajima, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qqy.cif.gz | 38.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qqy.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qqy_validation.pdf.gz | 359 KB | Display | wwPDB validaton report |
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Full document | 1qqy_full_validation.pdf.gz | 362.2 KB | Display | |
Data in XML | 1qqy_validation.xml.gz | 4 KB | Display | |
Data in CIF | 1qqy_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/1qqy ftp://data.pdbj.org/pub/pdb/validation_reports/qq/1qqy | HTTPS FTP |
-Related structure data
Related structure data | 1eqlS 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: 14621.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Plasmid: PLASMID PSCREEN 1-B(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P81708, lysozyme |
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#2: 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: 2.5 Å3/Da / Density % sol: 51.5 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, tri-sodium citrate, ammonium acetate, EDTA, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 25, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→100 Å / Num. obs: 13034 / % possible obs: 94.8 % / Observed criterion σ(I): 1 / Redundancy: 15.3 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.85→1.89 Å / Rmerge(I) obs: 0.25 / Num. unique all: 725 / % possible all: 82.2 |
Reflection | *PLUS Num. measured all: 199512 |
Reflection shell | *PLUS % possible obs: 82.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EQL Resolution: 1.85→8 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: THROUGHOUT / Bsol: 62.4 Å2 / ksol: 0.449 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.88 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 24
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | |||||||||||||||||||||||||
Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.007 |