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- PDB-3ild: Structure of ORF157-K57A from Acidianus filamentous virus 1 -

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Basic information

Entry
Database: PDB / ID: 3ild
TitleStructure of ORF157-K57A 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 / Uncharacterized protein ORF157
Function and homology information
Biological speciesAcidianus filamentous virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGoulet, A. / Lichiere, J. / 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
DepositionAug 7, 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 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)18,8282
Polymers18,8041
Non-polymers241
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)64.757, 64.757, 85.743
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-

MG

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Components

#1: Protein Putative uncharacterized protein / ORF157


Mass: 18803.508 Da / Num. of mol.: 1 / Mutation: K57A
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 8000, 0.2M MgCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 3.1→47 Å / Num. obs: 4047 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 80 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 29.2
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 12 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 6.8 / Num. unique all: 572 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3II2

3ii2


Resolution: 3.1→22 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.857 / SU B: 85.388 / SU ML: 0.644 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.566 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30932 227 5.7 %RANDOM
Rwork0.2711 ---
obs0.27335 3788 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.218 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å21.29 Å2-0 Å2
2--2.57 Å2-0 Å2
3----3.86 Å2
Refinement stepCycle: LAST / Resolution: 3.1→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 1 0 1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221303
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9371759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.085147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.41223.52968
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88515240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.175158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02984
X-RAY DIFFRACTIONr_mcbond_it0.4151.5739
X-RAY DIFFRACTIONr_mcangle_it0.78921203
X-RAY DIFFRACTIONr_scbond_it0.9543564
X-RAY DIFFRACTIONr_scangle_it1.6894.5556
LS refinement shellResolution: 3.101→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 15 -
Rwork0.362 255 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -37.8382 Å / Origin y: 15.6846 Å / Origin z: 5.2909 Å
111213212223313233
T0.3994 Å20.202 Å2-0.0267 Å2-0.3324 Å20.2498 Å2--0.3267 Å2
L11.3913 °2-2.0748 °2-4.2111 °2-7.7103 °21.6848 °2--8.5002 °2
S-0.8961 Å °-1.6989 Å °-1.3906 Å °-0.287 Å °0.6841 Å °1.1938 Å °0.7158 Å °0.5298 Å °0.212 Å °

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