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- PDB-2h36: Structure of ORF14 from Sulfolobus Islandicus Filamentous Virus (SIFV) -

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Basic information

Entry
Database: PDB / ID: 2h36
TitleStructure of ORF14 from Sulfolobus Islandicus Filamentous Virus (SIFV)
ComponentsHypothetical protein SIFV0014
KeywordsUNKNOWN FUNCTION / Archaea / Virus
Function / homologyDouble Stranded RNA Binding Domain - #300 / Sulfolobus islandicus filamentous virus, Orf14 / Protein of unknown function (DUF1374) / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein 14
Function and homology information
Biological speciesSulfolobus islandicus filamentous virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsGoulet, A. / Spinelli, S. / Cambillau, C.
Citation
Journal: Proteins / Year: 2009
Title: The crystal structure of ORF14 from Sulfolobus islandicus filamentous virus
Authors: Goulet, A. / Spinelli, S. / Blangy, S. / van Tilbeurgh, H. / Leulliot, N. / Basta, T. / Prangishvili, D. / Cambillau, C. / Campanacci, V.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary X-ray diffraction analysis of protein 14 from Sulfolobus islandicus filamentous virus (SIFV)
Authors: Goulet, A. / Spinelli, S. / Campanacci, V. / Porciero, S. / Blangy, S. / Garrett, R.A. / van Tilbeurgh, H. / Leulliot, N. / Basta, T. / Prangishvili, D. / Cambillau, C.
History
DepositionMay 22, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Hypothetical protein SIFV0014


Theoretical massNumber of molelcules
Total (without water)13,4811
Polymers13,4811
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.099, 68.099, 132.433
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Hypothetical protein SIFV0014 / ORF14


Mass: 13480.763 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus filamentous virus
Genus: Betalipothrixvirus / Gene: ORF 14 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q914L6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 18-26% (w/v) polyethylene glycol 4000, 0.5M MgCl2, 33mM HEPES, 0.2M imidazole malate pH 5.2-5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9798 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 4, 2006
RadiationMonochromator: 2 mirrors, onemonochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.95→23 Å / Num. obs: 4170 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 53.4 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 75
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 55 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 17 / Rsym value: 0.386 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
MOSFLMdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.95→22.07 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 37.162 / SU ML: 0.331 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 4.336 / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29442 406 9.8 %RANDOM
Rwork0.22711 ---
obs0.23353 3740 98.74 %-
all-4170 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.377 Å2
Baniso -1Baniso -2Baniso -3
1-5.14 Å22.57 Å20 Å2
2--5.14 Å20 Å2
3----7.71 Å2
Refinement stepCycle: LAST / Resolution: 2.95→22.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 0 5 923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022936
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9641261
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9845107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.23126.2556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.72315179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.07153
X-RAY DIFFRACTIONr_chiral_restr0.0980.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02722
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.2385
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.2622
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.41.5554
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7162873
X-RAY DIFFRACTIONr_scbond_it0.8633441
X-RAY DIFFRACTIONr_scangle_it1.4514.5388
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.952→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 30 -
Rwork0.377 257 -
obs--98.97 %
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)
14.71390.4815-1.50239.4201-0.4666.2145-0.1974-0.4937-0.00890.21810.2607-0.2675-0.25370.0258-0.0633-0.0086-0.0995-0.11220.34350.11020.237916.9845.95455.239
227.85424.286117.05786.75891.146714.79890.7979-1.56920.83851.0002-1.1119-0.08190.023-0.28340.3140.5413-0.08840.0510.3934-0.04091.057147.97410.71249.665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1XA17 - 10918 - 110
2X-RAY DIFFRACTION2XA2 - 163 - 17

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