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- PDB-4cdm: Crystal structure of M. mazei photolyase soaked with synthetic 8-HDF -

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Basic information

Entry
Database: PDB / ID: 4cdm
TitleCrystal structure of M. mazei photolyase soaked with synthetic 8-HDF
ComponentsDEOXYRIBODIPYRIMIDINE PHOTOLYASE
KeywordsLYASE / DNA REPAIR / ANTENNA CHROMOPHORE
Function / homology
Function and homology information


deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / DNA repair / nucleotide binding / DNA binding
Similarity search - Function
DNA photolyase class 2 / : / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / 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 ...DNA photolyase class 2 / : / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / 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 / Chem-FO1 / Deoxyribodipyrimidine photo-lyase
Similarity search - Component
Biological speciesMETHANOSARCINA MAZEI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.7 Å
AuthorsKiontke, S. / Batschauer, A. / Essen, L.-O.
CitationJournal: J.Biol.Chem. / Year: 2014
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
DepositionNov 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3May 8, 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.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 PHOTOLYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8419
Polymers55,1231
Non-polymers1,7178
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.890, 69.890, 245.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DEOXYRIBODIPYRIMIDINE PHOTOLYASE / CLASS II CPD PHOTOLYASE


Mass: 55123.480 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOSARCINA MAZEI (archaea) / Strain: GO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: Q8PYK9, deoxyribodipyrimidine photo-lyase

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Non-polymers , 5 types, 41 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-FO1 / 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol / 7,8-didemethyl-8-hydroxy-5-deazariboflavin


Mass: 363.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N3O7
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsFLAVIN-ADENINE DINUCLEOTIDE (FAD): NON-COVALENTLY BOUND. 8-HYDROXY-10-(D-RIBO-2,3,4, 5- ...FLAVIN-ADENINE DINUCLEOTIDE (FAD): NON-COVALENTLY BOUND. 8-HYDROXY-10-(D-RIBO-2,3,4, 5-TETRAHYDROXYPENTYL) -5-DEAZAISOALLOXAZINE (FO1): NON-COVALENTLY BOUND
Sequence detailsSEQUENCE CLONFLICT AT POSITION 377 (SEE BELOW)

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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: 2.68 Å3/Da / Density % sol: 54.21 % / Description: NONE
Crystal growDetails: 0.5 M LITHIUM SULFATE, 7.5% (W/V) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 15494 / % possible obs: 89.3 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5 / % possible all: 84.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.7→29.2 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.853 / SU B: 12.291 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 60 TO 64 HAVE ALTERNATIVE CONFORMATIONS, RESIDUES 190 TO 197 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.26997 216 1.4 %RANDOM
Rwork0.20596 ---
obs0.20686 15081 88.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.58 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 111 33 3783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223897
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9865294
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6445460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35623.743179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59115636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5311523
X-RAY DIFFRACTIONr_chiral_restr0.0880.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212965
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5141.52295
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00423684
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.29231602
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2544.51609
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 11 -
Rwork0.236 838 -
obs--82.99 %

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