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- PDB-1dnp: STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE -

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Basic information

Entry
Database: PDB / ID: 1dnp
TitleSTRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE
ComponentsDNA PHOTOLYASE
KeywordsLYASE (CARBON-CARBON) / DNA REPAIR / ELECTRON TRANSFER / EXCITATION ENERGY TRANSFER / LYASE / CARBON-CARBON
Function / homology
Function and homology information


photoreactive repair / deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / response to light stimulus / phototransduction, visible light / FAD binding / damaged DNA binding / DNA binding
Similarity search - Function
DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal ...DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID / Deoxyribodipyrimidine photo-lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsPark, H.-W. / Sancar, A. / Deisenhofer, J.
Citation
Journal: Science / Year: 1995
Title: Crystal structure of DNA photolyase from Escherichia coli.
Authors: Park, H.W. / Kim, S.T. / Sancar, A. / Deisenhofer, J.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary Crystallographic Analysis of Escherichia Coli DNA Photolyase
Authors: Park, H.W. / Sancar, A. / Deisenhofer, J.
History
DepositionJul 3, 1995Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA PHOTOLYASE
B: DNA PHOTOLYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6896
Polymers107,2032
Non-polymers2,4864
Water6,720373
1
A: DNA PHOTOLYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8453
Polymers53,6021
Non-polymers1,2432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA PHOTOLYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8453
Polymers53,6021
Non-polymers1,2432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.600, 72.200, 58.500
Angle α, β, γ (deg.)99.10, 101.50, 72.00
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.025044, -0.324306, -0.945621), (-0.323889, -0.897527, 0.299234), (-0.945763, 0.298782, -0.127517)
Vector: 77.66, 100.07, 50.02)

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Components

#1: Protein DNA PHOTOLYASE / DNA CYCLOBUTANE DIPYRIMIDINE PHOTOLYASE


Mass: 53601.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PHOTOREACTIVATING ENZYME / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P00914, deoxyribodipyrimidine photo-lyase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-MHF / 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID


Mass: 457.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N7O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 47 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion
Details: seeding. refer to Park, H.W., (1993) J.Mol.Biol., 231, 1122.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlphotolyase1drop
220 %glycerol1drop
350 mMTris-HCl1drop
530 %(w/v)PEG40001reservoir
60.9 M1reservoirLiCl
7100 mMTris-HCl1reservoir
4reservoir1drop

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Data collection

Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Oct 1, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 33086 / % possible obs: 78.3 % / Observed criterion σ(I): 2 / Redundancy: 2.45 % / Rmerge(I) obs: 0.043
Reflection
*PLUS
Num. measured all: 76311

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.3→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.246 --
Rwork0.172 --
obs0.172 32619 78.3 %
Displacement parametersBiso mean: 17.62 Å2
Refine analyzeLuzzati sigma a obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7538 0 172 373 8083
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39

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