+Open data
-Basic information
Entry | Database: PDB / ID: 2j4d | ||||||
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Title | Cryptochrome 3 from Arabidopsis thaliana | ||||||
Components | CRYPTOCHROME DASH | ||||||
Keywords | DNA BINDING PROTEIN / DNA-BINDING PROTEIN / CRYPTOCHROME / FLAVOPROTEIN / FAD / MITOCHONDRION / PLASTID / CHROMOPHORE / CHLOROPLAST / TRANSIT PEPTIDE / BLUE-LIGHT RESPONSE | ||||||
Function / homology | Function and homology information photoreactive repair / deoxyribodipyrimidine photo-lyase activity / photoreceptor activity / FAD binding / chloroplast / damaged DNA binding / mitochondrion / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Klar, T. / Pokorny, R. / Batschauer, A. / Essen, L.-O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Cryptochrome 3 from Arabidopsis Thaliana: Structural and Functional Analysis of its Complex with a Folate Light Antenna Authors: Klar, T. / Pokorny, R. / Moldt, J. / Batschauer, A. / Essen, L.-O. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Crystallization and Preliminary X-Ray Analysis of Cryptochrome 3 from Arabidopsis Thaliana Authors: Pokorny, R. / Klar, T. / Essen, L.-O. / Batschauer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j4d.cif.gz | 233.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j4d.ent.gz | 186.5 KB | Display | PDB format |
PDBx/mmJSON format | 2j4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j4d_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 2j4d_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 2j4d_validation.xml.gz | 48.9 KB | Display | |
Data in CIF | 2j4d_validation.cif.gz | 70 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/2j4d ftp://data.pdbj.org/pub/pdb/validation_reports/j4/2j4d | HTTPS FTP |
-Related structure data
Related structure data | 1np7S 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.88463, 0.39435, 0.24881), Vector: |
-Components
#1: Protein | Mass: 60332.621 Da / Num. of mol.: 2 Fragment: MATURE PROTEIN WITHOUT PLASTID IMPORT SEQUENCE, RESIDUES 45-569 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PQE-60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15-PREP4 / References: UniProt: Q84KJ5 #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: 2.48 Å3/Da / Density % sol: 44 % |
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Crystal grow | pH: 4.6 Details: 10 MG/ML PROTEIN, 85 MM NA-CITRATE PH 4.6, 170 MM NH4-ACETATE, 21.5 W/V-% PEG 4000 AND 7.5 V/V-% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8125 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8125 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 93259 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.47 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NP7 Resolution: 1.9→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: BULK / Bsol: 48.4007 Å2 / ksol: 0.357165 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 28
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Xplor file |
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