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- PDB-2j09: Thermus DNA photolyase with FMN antenna chromophore -

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Basic information

Entry
Database: PDB / ID: 2j09
TitleThermus DNA photolyase with FMN antenna chromophore
ComponentsDEOXYRIBODIPYRIMIDINE PHOTO-LYASE
KeywordsLYASE / FLAVOPROTEIN / DNA REPAIR
Function / homology
Function and homology information


deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / response to light stimulus / FAD binding / DNA repair / 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 / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Deoxyribodipyrimidine photo-lyase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKlar, T. / Kaiser, G. / Hennecke, U. / Carell, T. / Batschauer, A. / Essen, L.-O.
CitationJournal: Chembiochem / Year: 2006
Title: Natural and Non-Natural Antenna Chromophores in the DNA Photolyase from Thermus Thermophilus
Authors: Klar, T. / Kaiser, G. / Hennecke, U. / Carell, T. / Batschauer, A. / Essen, L.-O.
History
DepositionAug 1, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 25, 2017Group: Data collection
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: DEOXYRIBODIPYRIMIDINE PHOTO-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4416
Polymers47,9741
Non-polymers1,4675
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DEOXYRIBODIPYRIMIDINE PHOTO-LYASE
hetero molecules

A: DEOXYRIBODIPYRIMIDINE PHOTO-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,88212
Polymers95,9482
Non-polymers2,93510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6670 Å2
ΔGint-62.2 kcal/mol
Surface area34100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.433, 112.433, 140.141
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DEOXYRIBODIPYRIMIDINE PHOTO-LYASE / DNA PHOTOLYASE / PHOTOREACTIVATING ENZYME


Mass: 47973.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P61497, deoxyribodipyrimidine photo-lyase

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Non-polymers , 5 types, 240 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.46 %
Crystal growpH: 8.5
Details: 50 MM TRIS-HCL, PH 8.5, 1.0 M NH4 H2PO4, 11.8 MG/ML PROTEIN. CRYSTAL WAS SOAKED WITH 0.1 MM FMN FOR 90 MIN PRIOR TO FREEZING.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 2003 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→33.7 Å / Num. obs: 35872 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IQR

1iqr


Resolution: 2→19.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.277 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1776 5 %RANDOM
Rwork0.183 ---
obs0.185 33863 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20.8 Å20 Å2
2--1.6 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 95 235 3723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0213549
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6012.0044867
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1065418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.75721.333165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.03915500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1481543
X-RAY DIFFRACTIONr_chiral_restr0.1480.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.022814
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.21741
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.22357
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2980.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0631.52152
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.81323352
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.57631732
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.4194.51515
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 113
Rwork0.215 2288
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0134-0.54380.04850.6699-0.12511.2887-0.0457-0.06310.02040.02650.0989-0.03740.1255-0.2526-0.05330.0002-0.024-0.0176-0.00970.0091-0.002237.82315.78227.761
21.5501-0.51840.12733.3049-0.75472.4019-0.4062-0.485-0.01480.85180.5106-0.0337-0.1176-0.5259-0.10450.16170.2535-0.00450.21280.0282-0.118333.63915.77756.146
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 260
2X-RAY DIFFRACTION1A1422
3X-RAY DIFFRACTION2A261 - 420
4X-RAY DIFFRACTION2A1421

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