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- PDB-7f8t: Re-refinement of the 2XRY X-ray structure of archaeal class II CP... -

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Basic information

Entry
Database: PDB / ID: 7f8t
TitleRe-refinement of the 2XRY X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei
ComponentsDeoxyribodipyrimidine photolyase
KeywordsLYASE / Oxidoreductase / redox state / photoreduction / DNA BINDING PROTEIN
Function / homology
Function and homology information


photoreactive repair / deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / DNA binding
Similarity search - Function
DNA photolyase class 2 / : / 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 / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Deoxyribodipyrimidine photo-lyase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMaestre-Reyna, M. / Yang, C.-H. / Huang, W.C. / Nango, E. / Gusti-Ngurah-Putu, E.-P. / Franz-Badur, S. / Wu, W.-J. / Wu, H.-Y. / Wang, P.-H. / Liao, J.-H. ...Maestre-Reyna, M. / Yang, C.-H. / Huang, W.C. / Nango, E. / Gusti-Ngurah-Putu, E.-P. / Franz-Badur, S. / Wu, W.-J. / Wu, H.-Y. / Wang, P.-H. / Liao, J.-H. / Lee, C.-C. / Huang, K.-F. / Chang, Y.-K. / Weng, J.-H. / Sugahara, M. / Owada, S. / Joti, Y. / Tanaka, R. / Tono, K. / Kiontke, S. / Yamamoto, J. / Iwata, S. / Essen, L.-O. / Bessho, Y. / Tsai, M.-D.
Funding support Taiwan, Japan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)AS-KPQ-105-TPP Taiwan
Japan Society for the Promotion of Science (JSPS)16K01942 Japan
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
DepositionJul 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 0This entry 7f8t reflects an alternative modeling of the original structural data R2xrySF determined ...This entry 7f8t reflects an alternative modeling of the original structural data R2xrySF determined by authors of the PDB entry 2XRY: AUTHOR S.KIONTKE,Y.GEISSELBRECHT,R.POKORNY,T.CARELL,A.BATSCHAUER,L.O.ESSEN

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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)56,95813
Polymers55,1231
Non-polymers1,83412
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.770, 69.770, 243.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Deoxyribodipyrimidine photolyase


Mass: 55123.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0F8I5V2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.25 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2XRY.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.5 M LITHIUM SULFATE, 7.5% (W/V) PEG 8000

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Data collection

DiffractionSerial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.88567 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88567 Å / Relative weight: 1

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XRY

2xry


Resolution: 1.5→19.94 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 1305 1.5 %
Rwork0.17 --
obs0.1704 87280 89.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3677 0 110 375 4162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184016
X-RAY DIFFRACTIONf_angle_d1.4885487
X-RAY DIFFRACTIONf_dihedral_angle_d13.2381494
X-RAY DIFFRACTIONf_chiral_restr0.072571
X-RAY DIFFRACTIONf_plane_restr0.012693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.560.29821520.27559318X-RAY DIFFRACTION89
1.56-1.630.28831490.24389498X-RAY DIFFRACTION91
1.63-1.720.27241270.22119541X-RAY DIFFRACTION91
1.72-1.820.23081520.19269572X-RAY DIFFRACTION91
1.82-1.970.18021540.16799475X-RAY DIFFRACTION90
1.97-2.160.17291410.14799581X-RAY DIFFRACTION90
2.16-2.480.17181500.13879587X-RAY DIFFRACTION90
2.48-3.120.17991390.15029637X-RAY DIFFRACTION90
3.12-19.940.17981410.15699766X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: 18.6387 Å / Origin y: 24.7176 Å / Origin z: 104.7065 Å
111213212223313233
T0.051 Å20.009 Å2-0.007 Å2-0.0968 Å2-0.0059 Å2--0.0691 Å2
L1.045 °2-0.0249 °20.1478 °2-0.6051 °2-0.0341 °2--1.0687 °2
S-0.0271 Å °0.0873 Å °0.0005 Å °-0.0454 Å °-0.0066 Å °0.029 Å °-0.0058 Å °-0.0263 Å °0.0178 Å °
Refinement TLS groupSelection details: all

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