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- PDB-2xrz: X-ray structure of archaeal class II CPD photolyase from Methanos... -

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Entry
Database: PDB / ID: 2xrz
TitleX-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei in complex with intact CPD-lesion
Components
  • COUNTERSTRAND-OLIGONUCLEOTIDE
  • CPD-COMPRISING OLIGONUCLEOTIDE
  • DEOXYRIBODIPYRIMIDINE PHOTOLYASE
KeywordsLYASE/DNA / LYASE-DNA COMPLEX / PHOTOLYASE / DNA DAMAGE / DNA REPAIR / CLASS II / INTACT CPD-LESION / PROTEIN-DNA COMPLEX / WATER CLUSTER
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 / 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 ...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
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / DNA / DNA (> 10) / Deoxyribodipyrimidine photo-lyase
Similarity search - Component
Biological speciesMETHANOSARCINA MAZEI (archaea)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKiontke, S. / Geisselbrecht, Y. / Pokorny, R. / Carell, T. / Batschauer, A. / Essen, L.O.
CitationJournal: Embo J. / Year: 2011
Title: Crystal Structures of an Archaeal Class II DNA Photolyase and its Complex with Uv-Damaged Duplex DNA.
Authors: Kiontke, S. / Geisselbrecht, Y. / Pokorny, R. / Carell, T. / Batschauer, A. / Essen, L.O.
History
DepositionSep 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2May 1, 2024Group: 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_validate_polymer_linkage / struct_conn / struct_ncs_dom_lim / 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_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DEOXYRIBODIPYRIMIDINE PHOTOLYASE
B: DEOXYRIBODIPYRIMIDINE PHOTOLYASE
C: CPD-COMPRISING OLIGONUCLEOTIDE
D: COUNTERSTRAND-OLIGONUCLEOTIDE
E: CPD-COMPRISING OLIGONUCLEOTIDE
F: COUNTERSTRAND-OLIGONUCLEOTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,19618
Polymers127,8996
Non-polymers2,29812
Water11,440635
1
A: DEOXYRIBODIPYRIMIDINE PHOTOLYASE
C: CPD-COMPRISING OLIGONUCLEOTIDE
D: COUNTERSTRAND-OLIGONUCLEOTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,34312
Polymers63,9493
Non-polymers1,3949
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-34.8 kcal/mol
Surface area21730 Å2
MethodPISA
2
B: DEOXYRIBODIPYRIMIDINE PHOTOLYASE
E: CPD-COMPRISING OLIGONUCLEOTIDE
F: COUNTERSTRAND-OLIGONUCLEOTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8536
Polymers63,9493
Non-polymers9043
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-14.5 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.700, 116.200, 168.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISHISVALVAL6AA2 - 18620 - 204
211HISHISVALVAL6BB2 - 18620 - 204
112LYSLYSTYRTYR6AA221 - 461239 - 479
212LYSLYSTYRTYR6BB221 - 461239 - 479
122FADFADFADFAD4AG998
222FADFADFADFAD4BP998

NCS ensembles :
ID
1
2

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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 / Mutation: YES
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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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain CPD-COMPRISING OLIGONUCLEOTIDE


Mass: 4520.021 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: OLIGONUCLEOTIDE WITH A SYNTHETIC FORMACETAL- LINKED THYMINE DIMER
Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain COUNTERSTRAND-OLIGONUCLEOTIDE


Mass: 4305.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 5 types, 647 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 377 TO THR ENGINEERED RESIDUE IN CHAIN B, MET 377 TO THR
Nonpolymer details[(1R,3R,4S,9R,10S,12R,15AS,15BR,18BR,18CS)-10-HYDROXY-15A, 15B-DIMETHYL-13,15,16,18- ...[(1R,3R,4S,9R,10S,12R,15AS,15BR,18BR,18CS)-10-HYDROXY-15A, 15B-DIMETHYL-13,15,16,18-TETRAOXOHEXADECAHYDRO-8H-9, 12-EPOXY-1,4-METHANO-2,5,7-TRIOXA-12A,14,17, 18A-TETRAAZACYCLOHEXADECA[1,2,3, 4-DEF]BIPHENYLEN-3-YL]METHYL DIHYDROGEN PHOSPHATE (TT): SYNTHETIC CPD-LESION WITH FORMACETAL LINKAGE

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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: 2.73 Å3/Da / Density % sol: 59.75 % / Description: NONE
Crystal growpH: 4.6
Details: 0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.6, 10% (W/V) PEG 4000, 10% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: May 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→29.48 Å / Num. obs: 72130 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURAL DATA OF NATIVE M. MAZEI PHOTOLYASE.

Resolution: 2.2→29.48 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.385 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. RESIDUES A187-A197 AND B188-B220 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.20819 1094 1.5 %SHELLS
Rwork0.17036 ---
obs0.17093 70962 99.94 %-
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: 47.114 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2---1.36 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7125 1017 153 635 8930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228681
X-RAY DIFFRACTIONr_bond_other_d0.0010.025641
X-RAY DIFFRACTIONr_angle_refined_deg1.3632.12211973
X-RAY DIFFRACTIONr_angle_other_deg0.952313733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.375900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2823.778360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.769151244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6831546
X-RAY DIFFRACTIONr_chiral_restr0.0710.21240
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021685
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_it0.461.54458
X-RAY DIFFRACTIONr_mcbond_other0.1131.51782
X-RAY DIFFRACTIONr_mcangle_it0.88727158
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.38934221
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1774.54805
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
21A71medium positional0.060.5
22B71medium positional0.060.5
11A2474loose positional0.515
12B2474loose positional0.515
21A3309loose positional0.545
22B3309loose positional0.545
21A71medium thermal0.572
22B71medium thermal0.572
11A2474loose thermal2.2710
12B2474loose thermal2.2710
21A3309loose thermal0.5110
22B3309loose thermal0.5110
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 73 -
Rwork0.25 5166 -
obs--99.96 %
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)
11.42220.27890.09911.54520.09941.4054-0.08380.30490.3588-0.37280.1169-0.0011-0.18590.0527-0.03310.1043-0.04060.00310.11210.10030.2079-14.115827.0272-20.2772
20.88570.0881-0.09831.87380.3260.9472-0.015-0.02750.17850.05230.02240.09810.1126-0.0292-0.00740.0064-0.0018-0.00340.07230.00050.1107-21.601911.9319-1.3713
32.29581.8424-0.9633.1701-0.94691.5314-0.05220.1348-0.0645-0.04320.12410.04340.1496-0.123-0.07190.1171-0.0528-0.0080.02670.00480.0364-35.0473-28.4179-10.1222
41.73551.5522-0.41213.0457-0.80291.5034-0.39680.54750.0545-0.7430.50250.13390.2584-0.229-0.10570.3391-0.1642-0.00990.32180.01530.0253-27.9067-12.5513-30.5247
59.0282-1.177-1.27856.44911.69467.8991-0.4731-1.18710.77891.21380.7377-0.89880.750.8886-0.26450.27230.1659-0.1650.3169-0.15390.2193-2.58074.05110.6582
66.6912-0.211-0.56534.44561.01138.63210.05650.9577-0.7076-0.68920.0072-0.59871.02090.7825-0.06370.57560.02540.15910.5151-0.13660.1671-9.8652-15.9506-42.1444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 186
2X-RAY DIFFRACTION2A198 - 998
3X-RAY DIFFRACTION3B2 - 187
4X-RAY DIFFRACTION4B221 - 998
5X-RAY DIFFRACTION5C3 - 14
6X-RAY DIFFRACTION5D1 - 14
7X-RAY DIFFRACTION6E4 - 14
8X-RAY DIFFRACTION6F1 - 13

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