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- PDB-3ii2: Structure of ORF157 from Acidianus Filamentous Virus 1 -

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Basic information

Entry
Database: PDB / ID: 3ii2
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 / SAD / Resolution: 2 Å
AuthorsGoulet, A. / Porciero, S. / 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
SupersessionMar 23, 2010ID: 2OQ8
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,63710
Polymers18,8621
Non-polymers7769
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.637, 65.637, 85.568
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-164-

NI

21A-165-

NI

31A-298-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 125 molecules

#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NI / NICKEL (II) ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
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: ID14-4 / Wavelength: 1.005 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14251 / % possible obs: 96.3 % / Redundancy: 6 % / Biso Wilson estimate: 27.06 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 6.3 / % possible all: 96.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.4_153refinement
RefinementMethod to determine structure: SAD / Resolution: 2→47.348 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.906 / FOM work R set: 0.887 / SU ML: 0.22 / σ(F): 0.12 / Phase error: 17.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 852 6.01 %
Rwork0.1697 --
obs0.1735 14181 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.513 Å2 / ksol: 0.414 e/Å3
Displacement parametersBiso max: 81.44 Å2 / Biso mean: 32.986 Å2 / Biso min: 12.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.303 Å20 Å20 Å2
2---0.303 Å2-0 Å2
3---0.606 Å2
Refinement stepCycle: LAST / Resolution: 2→47.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 0 14 116 1415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011363
X-RAY DIFFRACTIONf_angle_d1.141845
X-RAY DIFFRACTIONf_dihedral_angle_d15.951513
X-RAY DIFFRACTIONf_chiral_restr0.084193
X-RAY DIFFRACTIONf_plane_restr0.005230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.1250.2051390.1472175231495
2.125-2.2890.1921470.1382192233996
2.289-2.520.2091460.1492221236796
2.52-2.8840.2261420.1572237237997
2.884-3.6340.2311450.1572271241697
3.634-47.3610.2751330.1962233236691
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)
11.83-0.33370.13891.2-0.30522.2754-0.0137-0.0285-0.4175-0.06180.03970.02140.23490.187-0.00010.14270.0397-0.0040.13970.01610.164327.01814.39383.4872
20.36520.2947-0.09590.3033-0.23140.33310.0437-0.28990.05620.10680.0959-0.4331-0.11630.56130.00050.18710.0263-0.03980.29880.02250.216834.103820.108710.7253
31.45340.08721.44161.35160.69532.5074-0.0682-0.2209-0.0752-0.15090.0985-0.06070.0428-0.01141.73420.15460.07360.03640.20380.03540.128124.914923.179610.6642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 5:105)A5 - 105
2X-RAY DIFFRACTION2(chain A and resid 106:123)A106 - 123
3X-RAY DIFFRACTION3(chain A and resid 124:154)A124 - 154

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