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Yorodumi- PDB-1u3d: Crystal Structure of the PHR domain of Cryptochrome 1 from Arabid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u3d | ||||||
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Title | Crystal Structure of the PHR domain of Cryptochrome 1 from Arabidopsis thaliana with AMPPNP bound | ||||||
Components | Cryptochrome 1 apoprotein | ||||||
Keywords | SIGNALING PROTEIN / photolyase / AMPPNP | ||||||
Function / homology | Function and homology information detection of light stimulus / photoprotection / singlet oxygen-mediated programmed cell death / negative regulation of lateral root development / positive regulation of shade avoidance / positive regulation of systemic acquired resistance / regulation of secondary cell wall biogenesis / regulation of unidimensional cell growth / plant organ development / response to red light ...detection of light stimulus / photoprotection / singlet oxygen-mediated programmed cell death / negative regulation of lateral root development / positive regulation of shade avoidance / positive regulation of systemic acquired resistance / regulation of secondary cell wall biogenesis / regulation of unidimensional cell growth / plant organ development / response to red light / auxin transport / flavin adenine dinucleotide metabolic process / response to absence of light / circadian regulation of calcium ion oscillation / anthocyanin-containing compound metabolic process / response to strigolactone / regulation of meristem growth / response to low fluence blue light stimulus by blue low-fluence system / regulation of leaf morphogenesis / blue light signaling pathway / positive regulation of anion channel activity / response to far red light / response to magnetism / phototropism / response to high light intensity / photomorphogenesis / stomatal movement / positive regulation of defense response to bacterium / response to blue light / deoxyribodipyrimidine photo-lyase activity / blue light photoreceptor activity / regulation of hydrogen peroxide metabolic process / response to water deprivation / regulation of reactive oxygen species metabolic process / response to temperature stimulus / entrainment of circadian clock by photoperiod / response to light stimulus / FAD binding / circadian regulation of gene expression / regulation of circadian rhythm / PML body / defense response / circadian rhythm / kinase activity / regulation of gene expression / protein autophosphorylation / nuclear body / protein kinase activity / protein homodimerization activity / DNA binding / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Brautigam, C.A. / Smith, B.S. / Ma, Z. / Palnitkar, M. / Tomchick, D.R. / Machius, M. / Deisenhofer, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana. Authors: Brautigam, C.A. / Smith, B.S. / Ma, Z. / Palnitkar, M. / Tomchick, D.R. / Machius, M. / Deisenhofer, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u3d.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u3d.ent.gz | 90.5 KB | Display | PDB format |
PDBx/mmJSON format | 1u3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u3d_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1u3d_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1u3d_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 1u3d_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/1u3d ftp://data.pdbj.org/pub/pdb/validation_reports/u3/1u3d | HTTPS FTP |
-Related structure data
Related structure data | 1u3cC 1dnpS C: citing same article (ref.) 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 57599.879 Da / Num. of mol.: 1 / Fragment: PHR domain, residues 1-509 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: PMAL-C2-ATCRY / Production host: Escherichia coli (E. coli) / References: UniProt: Q43125 |
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-Non-polymers , 6 types, 92 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-FAD / | #5: Chemical | ChemComp-ANP / | #6: Chemical | ChemComp-NDS / | #7: 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: 3.7 Å3/Da / Density % sol: 67 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: glycerol, MES, sulfobetaine-195, 1,6-hexanediol, sodium, potassium tartrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.999 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Feb 21, 2004 |
Radiation | Monochromator: Double-crystal monochromator, Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. all: 32456 / Num. obs: 32456 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 37.6 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 3 / Num. unique all: 2955 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: E.coli photolyase (PDB entry 1DNP) Resolution: 2.45→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 333957.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: If no electron density was observed for the side chain of a residue, the occupancy for the side-chain atoms was set to 0.00. The occupancy of the ANP molecule was refined because of possible ...Details: If no electron density was observed for the side chain of a residue, the occupancy for the side-chain atoms was set to 0.00. The occupancy of the ANP molecule was refined because of possible competition for the binding site with 1,6-hexanediol.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.517 Å2 / ksol: 0.33839 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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