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- PDB-4pii: Crystal structure of hypothetical protein PF0907 from pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 4pii
TitleCrystal structure of hypothetical protein PF0907 from pyrococcus furiosus solved by sulfur SAD using Swiss light source data
ComponentsN-glycosylase/DNA lyase
KeywordsUNKNOWN FUNCTION / SULFUR SAD / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / STRUCTURAL GENOMICS / SECSG
Function / homology
Function and homology information


oxidized base lesion DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair
Similarity search - Function
N-glycosylase/DNA lyase-like / N-glycosylase/DNA lyase / N-glycosylase/DNA lyase / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / DNA glycosylase / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17 Å
AuthorsWeinert, T. / Waltersperger, S. / Olieric, V. / Panepucci, E. / Chen, L. / Rose, J.P. / Wang, M. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Nat.Methods / Year: 2015
Title: Fast native-SAD phasing for routine macromolecular structure determination.
Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / ...Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / Bargsten, K. / Prota, A.E. / Surana, P. / Kottur, J. / Nair, D.T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Boland, A. / Weichenrieder, O. / Wang, B.C. / Steinmetz, M.O. / Caffrey, M. / Wang, M.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,68611
Polymers29,2981
Non-polymers38810
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.430, 98.430, 65.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

21A-429-

HOH

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Components

#1: Protein N-glycosylase/DNA lyase / 8-oxoguanine DNA glycosylase / AGOG / DNA-(apurinic or apyrimidinic site) lyase / AP lyase


Mass: 29298.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0904 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8U2D5, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.3
Details: 0.1 M HEPES buffer containing 3.5M NaCl at pH 7.3. MODIFIED MICROBATCH, TEMPERATURE 291K
PH range: 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.066 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.066 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 23632 / % possible obs: 90.4 % / Redundancy: 15.4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 40.45

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SHELXDEphasing
Cootmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.17→49.215 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2.28 / Phase error: 25.55 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 2230 10.07 %RANDOM
Rwork0.1728 ---
obs0.1788 22138 86.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→49.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 14 71 1989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081956
X-RAY DIFFRACTIONf_angle_d1.0832649
X-RAY DIFFRACTIONf_dihedral_angle_d13.618714
X-RAY DIFFRACTIONf_chiral_restr0.04294
X-RAY DIFFRACTIONf_plane_restr0.006330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.2020.339780.321896X-RAY DIFFRACTION6
2.202-2.25330.2818640.1913526X-RAY DIFFRACTION37
2.2533-2.30960.27291100.1824900X-RAY DIFFRACTION65
2.3096-2.37210.26271360.18031254X-RAY DIFFRACTION86
2.3721-2.44190.24551600.18161404X-RAY DIFFRACTION98
2.4419-2.52070.26871600.18321428X-RAY DIFFRACTION100
2.5207-2.61080.2861700.1911394X-RAY DIFFRACTION100
2.6108-2.71530.26761520.17331452X-RAY DIFFRACTION100
2.7153-2.83890.23431580.21400X-RAY DIFFRACTION100
2.8389-2.98850.28061680.19991450X-RAY DIFFRACTION100
2.9885-3.17570.29991560.20331424X-RAY DIFFRACTION100
3.1757-3.42090.22641400.20081444X-RAY DIFFRACTION100
3.4209-3.7650.26571520.16891458X-RAY DIFFRACTION100
3.765-4.30950.21141440.14931446X-RAY DIFFRACTION100
4.3095-5.42850.20382020.15061396X-RAY DIFFRACTION100
5.4285-49.22780.17291500.15131436X-RAY DIFFRACTION100

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