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- PDB-4cdn: Crystal structure of M. mazei photolyase with its in vivo reconst... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cdn | ||||||
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Title | Crystal structure of M. mazei photolyase with its in vivo reconstituted 8-HDF antenna chromophore | ||||||
![]() | DEOXYRIBODIPYRIMIDINE PHOTOLYASE | ||||||
![]() | LYASE / PHOTOLYASE / DNA REPAIR / METHANOSARCINA MAZEI / ANTENNA CHROMOPHORE / 8-HDF / FAD | ||||||
Function / homology | ![]() photoreactive repair / deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kiontke, S. / Batschauer, A. / Essen, L.-O. | ||||||
![]() | ![]() Title: Structural and Evolutionary Aspects of Antenna Chromophore Usage by Class II Photolyases. Authors: Kiontke, S. / Gnau, P. / Haselsberger, R. / Batschauer, A. / Essen, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 393.3 KB | Display | ![]() |
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PDB format | ![]() | 320.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 42.2 KB | Display | |
Data in CIF | ![]() | 61.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cdmC ![]() 2xryS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 55123.480 Da / Num. of mol.: 2 / Fragment: RESIDUES 3-464 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8PYK9, deoxyribodipyrimidine photo-lyase |
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-Non-polymers , 7 types, 708 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/FO1.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FO1.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PEG / #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | FLAVIN-ADENINE DINUCLEOTIDE (FAD): NON-COVALENTLY BOUND. 8-HYDROXY-10-(D-RIBO-2,3,4, 5- ...FLAVIN-ADENINE DINUCLEOTI |
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Sequence details | SEQUENCE CONFLICT AT POSITION 377 (SEE BELOW) |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.7 % / Description: NONE |
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Crystal grow | Details: 0.1 M LITHIUM SULFATE, 0.1 M TRI-SODIUM CITRATE PH 5.6, 12% (W/V) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35 Å / Num. obs: 99823 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.2 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XRY Resolution: 1.9→34.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.059 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED, RESIDUES A191 TO A194 AND B189 TO B217 ARE DISORDERED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.085 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→34.47 Å
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Refine LS restraints |
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