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- PDB-1skv: Crystal Structure of D-63 from Sulfolobus Spindle Virus 1 -

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Basic information

Entry
Database: PDB / ID: 1skv
TitleCrystal Structure of D-63 from Sulfolobus Spindle Virus 1
ComponentsHypothetical 7.5 kDa protein
KeywordsVIRAL PROTEIN / Sulfolobus Spindle Virus / SSV / Archaeal / Crenarchaeal / Helix-Turn-Helix / Four Helix Bundle
Function / homologyHypothetical protein D-63 / : / Sulfolobus spindle-shape virus 1, protein D-63 / Helix hairpin bin / Helix hairpin bin domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Protein D-63
Function and homology information
Biological speciesSulfolobus virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsKraft, P. / Kummel, D. / Oeckinghaus, A. / Gauss, G.H. / Wiedenheft, B. / Young, M. / Lawrence, C.M.
CitationJournal: J.Virol. / Year: 2004
Title: Structure of d-63 from sulfolobus spindle-shaped virus 1: surface properties of the dimeric four-helix bundle suggest an adaptor protein function
Authors: Kraft, P. / Oeckinghaus, A. / Gauss, G.H. / Wiedenheft, B. / Young, M. / Lawrence, C.M.
History
DepositionMar 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical 7.5 kDa protein
B: Hypothetical 7.5 kDa protein
C: Hypothetical 7.5 kDa protein
D: Hypothetical 7.5 kDa protein


Theoretical massNumber of molelcules
Total (without water)33,6104
Polymers33,6104
Non-polymers00
Water18010
1
A: Hypothetical 7.5 kDa protein
B: Hypothetical 7.5 kDa protein


Theoretical massNumber of molelcules
Total (without water)16,8052
Polymers16,8052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-20 kcal/mol
Surface area7880 Å2
MethodPISA
2
C: Hypothetical 7.5 kDa protein
D: Hypothetical 7.5 kDa protein


Theoretical massNumber of molelcules
Total (without water)16,8052
Polymers16,8052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-22 kcal/mol
Surface area7020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.650, 110.650, 47.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
DetailsThe biological assembly is the AB dimer / The biological assembly is the CD dimer

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Components

#1: Protein
Hypothetical 7.5 kDa protein / ORF D-63


Mass: 8402.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus virus 1 / Genus: Fusellovirus / Gene: D-63 / Plasmid: pDest14 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P20215
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.99 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Ammonium Sulfate, ammonium acetate, PEG 4000, NaCl, Tris, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9778, 0.9787, 0.9789
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 16, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97781
20.97871
30.97891
ReflectionResolution: 2.6→20 Å / Num. all: 10225 / Num. obs: 10095 / % possible obs: 98.7 % / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 42
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 9 / Num. unique all: 1121 / % possible all: 99.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→15 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2695 490 -random
Rwork0.2222 ---
all0.2245 9704 --
obs0.2245 9704 98.89 %-
Displacement parametersBiso mean: 58 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å21.05 Å2-1.57 Å2
2--0.52 Å20 Å2
3---0 Å2
Refine analyze
ObsFree
Luzzati coordinate error0.654 Å-
Luzzati sigma a0.212 Å0.326 Å
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 0 10 2016
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.534
X-RAY DIFFRACTIONr_bond_refined_d0.016

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