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- PDB-4cdn: Crystal structure of M. mazei photolyase with its in vivo reconst... -

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Basic information

Entry
Database: PDB / ID: 4cdn
TitleCrystal structure of M. mazei photolyase with its in vivo reconstituted 8-HDF antenna chromophore
ComponentsDEOXYRIBODIPYRIMIDINE PHOTOLYASE
KeywordsLYASE / PHOTOLYASE / DNA REPAIR / METHANOSARCINA MAZEI / ANTENNA CHROMOPHORE / 8-HDF / FAD
Function / homology
Function and homology information


photoreactive repair / deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA photolyase class 2 / : / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / 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 / : / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / 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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Deoxyribodipyrimidine photo-lyase
Similarity search - Component
Biological speciesMETHANOSARCINA MAZEI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.3Dec 20, 2023Group: Data collection / Database references ...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 / 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
B: DEOXYRIBODIPYRIMIDINE PHOTOLYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,01820
Polymers110,2472
Non-polymers3,77118
Water12,430690
1
A: DEOXYRIBODIPYRIMIDINE PHOTOLYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,37013
Polymers55,1231
Non-polymers2,24612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DEOXYRIBODIPYRIMIDINE PHOTOLYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6497
Polymers55,1231
Non-polymers1,5256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.970, 114.740, 141.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DEOXYRIBODIPYRIMIDINE PHOTOLYASE / CLASS II CPD PHOTOLYASE


Mass: 55123.480 Da / Num. of mol.: 2 / 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 , 7 types, 708 molecules

#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-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.: 2 / Source method: obtained synthetically / Formula: C16H17N3O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / 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- -5-DEAZAISOALLOXAZINE (HDF): NON-COVALENTLY BOUND
Sequence detailsSEQUENCE CONFLICT 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: 2.91 Å3/Da / Density % sol: 57.7 % / Description: NONE
Crystal growDetails: 0.1 M LITHIUM SULFATE, 0.1 M TRI-SODIUM CITRATE PH 5.6, 12% (W/V) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XRY

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
RfactorNum. reflection% reflectionSelection details
Rfree0.17844 2022 2 %SHELLS
Rwork0.14857 ---
obs0.14916 97726 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.085 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2--1.86 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7253 0 251 690 8194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197794
X-RAY DIFFRACTIONr_bond_other_d0.0010.027171
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.98810579
X-RAY DIFFRACTIONr_angle_other_deg0.799316586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3545929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99223.934366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.173151284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4281546
X-RAY DIFFRACTIONr_chiral_restr0.0810.21092
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021802
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 135 -
Rwork0.261 7154 -
obs--98.5 %
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)
10.62210.0256-0.02760.46860.19941.18650.00310.12650.0145-0.0749-0.02250.0284-0.01910.01590.01940.04140.0123-0.01130.0569-0.00120.038564.70595.40335.269
20.5778-0.0830.20880.32810.23510.91550.0052-0.090.01490.0355-0.0101-0.01130.0474-0.02630.00490.0481-0.0007-0.00830.0587-0.00050.042367.6796.23959.892
31.2269-0.01620.0510.65620.03741.2345-0.0033-0.4061-0.10210.04630.0058-0.0083-0.0426-0.0119-0.00240.01160.02380.01210.2130.0770.032429.186111.6548.304
41.0279-0.2589-0.23830.4227-0.08240.85750.0227-0.0003-0.0615-0.0739-0.01330.0490.0139-0.0259-0.00930.03890.0124-0.01130.05230.0440.052931.197113.07122.197
51.7057-2.1214-0.19945.2690.14161.27480.0527-0.1311-0.11850.10610.171-0.03070.1393-0.3148-0.22370.1082-0.0168-0.02450.150.03640.118865.31391.85756.501
67.75622.8525-3.49163.88622.10416.06110.19590.43850.22110.1890.16220.01340.00360.0073-0.35810.1032-0.01130.00280.1392-0.02930.10571.193101.18242.844
711.3225-4.514-0.00862.0170.32450.47530.04190.1528-0.11030.0041-0.10710.0950.0364-0.07750.06520.12290.0054-0.00030.15390.05280.147627.075112.01527.092
84.8408-0.49281.91194.2055-3.657810.4064-0.0366-0.3346-0.07810.023-0.0579-0.0272-0.02850.17170.09450.014-0.00520.00450.16810.04880.037935.382118.15941.127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 188
2X-RAY DIFFRACTION2A195 - 462
3X-RAY DIFFRACTION3B1 - 188
4X-RAY DIFFRACTION4B218 - 462
5X-RAY DIFFRACTION5A998
6X-RAY DIFFRACTION6A999
7X-RAY DIFFRACTION7B998
8X-RAY DIFFRACTION8B999

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