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Yorodumi- PDB-1tez: COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tez | ||||||
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Title | COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS | ||||||
Components |
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Keywords | LYASE/DNA / PHOTOLYASE / DNA REPAIR / LIGHT-DRIVEN ELECTRON TRANSFER / LYASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / nucleotide binding / DNA repair / DNA binding Similarity search - Function | ||||||
Biological species | Synechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Essen, L.-O. / Carell, T. / Mees, A. / Klar, T. | ||||||
Citation | Journal: Science / Year: 2004 Title: Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair Authors: Mees, A. / Klar, T. / Gnau, P. / Hennecke, U. / Eker, A.P.M. / Carell, T. / Essen, L.-O. #1: Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal Structure of DNA Photolyase from Anacystis Authors: Tamada, T. / Kitadokoro, K. / Higuchi, Y. / Inaka, K. / Yasui, A. / De Ruiter, P.E. / Eker, A.P. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tez.cif.gz | 459 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tez.ent.gz | 368.1 KB | Display | PDB format |
PDBx/mmJSON format | 1tez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/1tez ftp://data.pdbj.org/pub/pdb/validation_reports/te/1tez | HTTPS FTP |
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-Related structure data
Related structure data | 1qnfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-DNA chain , 4 types, 8 molecules IKJLMONP
#1: DNA chain | Mass: 3259.219 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Formacetal linkage replaces phosphate linkage between T7 and T8 of chains I and K #2: DNA chain | Mass: 2749.825 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: DNA chain | Mass: 1166.805 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: DNA chain | Mass: 1505.025 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Protein , 1 types, 4 molecules ABCD
#5: Protein | Mass: 53474.418 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: SYNTHETIC DNA OLIGONUCLEOTIDES ENGINEERED AS COUNTERSTRAND Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 6301 / Cellular location: CYTOPLASM / Gene: PHR / Plasmid: PET3A / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) References: UniProt: P05327, deoxyribodipyrimidine photo-lyase |
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-Non-polymers , 7 types, 1632 molecules
#6: Chemical | #7: Chemical | ChemComp-C / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-FAD / #11: Chemical | ChemComp-HDF / #12: Water | ChemComp-HOH / | |
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-Details
Compound details | COMPOUND THE CYCLOBUTANNonpolymer details | HETEROGEN DESOXYTHYM | |
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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: 2.44 Å3/Da / Density % sol: 49.2 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, magnesium chloride, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9796 / Wavelength: 0.9796 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 27, 2004 / Details: MIRRORS |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 218105 / Num. obs: 218105 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.1 / % possible all: 81.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QNF Resolution: 1.8→29.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 2423887.54 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.7551 Å2 / ksol: 0.37764 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→29.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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