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Yorodumi- PDB-1np7: Crystal Structure Analysis of Synechocystis sp. PCC6803 cryptochrome -
+Open data
-Basic information
Entry | Database: PDB / ID: 1np7 | ||||||
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Title | Crystal Structure Analysis of Synechocystis sp. PCC6803 cryptochrome | ||||||
Components | DNA photolyase | ||||||
Keywords | LYASE / protein with FAD cofactor | ||||||
Function / homology | Function and homology information DNA photolyase activity / photoreactive repair / FAD binding / DNA binding Similarity search - Function | ||||||
Biological species | Synechocystis sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Brudler, R. / Hitomi, K. / Daiyasu, H. / Toh, H. / Kucho, K. / Ishiura, M. / Kanehisa, M. / Roberts, V.A. / Todo, T. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 Title: Identification of a new cryptochrome class: structure, function, and evolution Authors: Brudler, R. / Hitomi, K. / Daiyasu, H. / Toh, H. / Kucho, K. / Ishiura, M. / Kanehisa, M. / Roberts, V.A. / Todo, T. / Tainer, J.A. / Getzoff, E.D. | ||||||
History |
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Remark 999 | SEQUENCE Residues 1-37 are not cloning artifacts and belong to the protein structure. The ...SEQUENCE Residues 1-37 are not cloning artifacts and belong to the protein structure. The discrepancy arises because the entry S74805 in GenBank is missing the first N-terminal 37 residues. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1np7.cif.gz | 215.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1np7.ent.gz | 170.6 KB | Display | PDB format |
PDBx/mmJSON format | 1np7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1np7_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1np7_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1np7_validation.xml.gz | 41.9 KB | Display | |
Data in CIF | 1np7_validation.cif.gz | 57.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/1np7 ftp://data.pdbj.org/pub/pdb/validation_reports/np/1np7 | HTTPS FTP |
-Related structure data
Related structure data | 1dnpS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 57111.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Plasmid: pGEX 4T-2, PCC6803 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P77967 #2: Chemical | #3: Chemical | #4: 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: 2.59 Å3/Da / Density % sol: 52.56 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20-24 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 3, 2000 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 88628 / Num. obs: 88628 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 8731 / Rsym value: 0.311 / % possible all: 95.8 |
Reflection | *PLUS Lowest resolution: 30 Å |
Reflection shell | *PLUS % possible obs: 95.8 % / Rmerge(I) obs: 0.311 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DNP Resolution: 1.9→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.91 Å | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |