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- PDB-3ii3: Structure of ORF157 from Acidianus filamentous Virus 1 -

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Basic information

Entry
Database: PDB / ID: 3ii3
TitleStructure of ORF157 from Acidianus filamentous Virus 1
ComponentsPutative uncharacterized protein
KeywordsDNA BINDING PROTEIN / virus / archaea / nuclease
Function / homologyProtein of unknown function DUF3258 / Protein of unknown function DUF3258 / Immunoglobulin-like - #2930 / Immunoglobulin-like / Sandwich / Mainly Beta / NICKEL (II) ION / Uncharacterized protein ORF157
Function and homology information
Biological speciesAcidianus filamentous virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGoulet, A. / Redder, P. / Pina, M. / Prangishvili, D. / van Tilbeurgh, H. / Cambillau, C. / Campanacci, V.
CitationJournal: J.Virol. / Year: 2010
Title: ORF157 from the archaeal virus Acidianus filamentous virus 1 defines a new class of nuclease
Authors: Goulet, A. / Pina, M. / Redder, P. / Prangishvili, D. / Vera, L. / Lichiere, J. / Leulliot, N. / van Tilbeurgh, H. / Ortiz-Lombardia, M. / Campanacci, V. / Cambillau, C.
History
DepositionJul 31, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0714
Polymers18,8621
Non-polymers2093
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.445, 65.445, 85.604
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-158-

NI

21A-159-

NI

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Components

#1: Protein Putative uncharacterized protein / ORF157


Mass: 18861.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TEV cleavage site inserted between attB1 and the gene of interest
Source: (gene. exp.) Acidianus filamentous virus 1 / Gene: AFV1 orf157 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q70LE6
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.9M LiSO4, 0.01M NiCl2, 0.1M Tris, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.891
11h+k,-k,-l20.109
ReflectionResolution: 2.7→40 Å / Num. obs: 6151 / % possible obs: 100 % / Redundancy: 5.2 % / Biso Wilson estimate: 78.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.1 / Num. unique all: 873 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3II2

3ii2


Resolution: 2.7→25 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.916 / SU B: 41.278 / SU ML: 0.367 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28144 356 5.8 %RANDOM
Rwork0.26992 ---
obs0.27057 5764 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.744 Å2
Baniso -1Baniso -2Baniso -3
1-52.07 Å20 Å2-0 Å2
2--52.07 Å20 Å2
3----104.14 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 0 8 0 1293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221334
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9421799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25623.33369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.0515249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.565159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021001
X-RAY DIFFRACTIONr_mcbond_it0.421.5752
X-RAY DIFFRACTIONr_mcangle_it0.74321227
X-RAY DIFFRACTIONr_scbond_it1.3323582
X-RAY DIFFRACTIONr_scangle_it1.9824.5571
LS refinement shellResolution: 2.699→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 27 -
Rwork0.322 389 -
obs--97.88 %
Refinement TLS params.Method: refined / Origin x: 27.1227 Å / Origin y: 16.2577 Å / Origin z: 5.4136 Å
111213212223313233
T0.0495 Å20.0057 Å2-0.0443 Å2-0.2245 Å20.1669 Å2--0.5895 Å2
L5.9978 °20.4145 °2-1.406 °2-4.1073 °21.806 °2--8.145 °2
S-0.3095 Å °-0.9879 Å °-0.389 Å °-0.3461 Å °0.3612 Å °0.2686 Å °0.1194 Å °0.1751 Å °-0.0516 Å °

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