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- PDB-1tbx: Crystal structure of SSV1 F-93 -

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Basic information

Entry
Database: PDB / ID: 1tbx
TitleCrystal structure of SSV1 F-93
ComponentsHypothetical 11.0 kDa protein
KeywordsVIRAL PROTEIN / Sulfolobus Spindle Virus / Winged Helix / F-93 / fusellovirus
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DNA binding / Orthogonal Bundle / Mainly Alpha / Protein F-93
Function and homology information
Biological speciesSulfolobus virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsKraft, P. / Oeckinghaus, A. / Kummel, D. / Gauss, G.H. / Wiedenheft, B. / Young, M. / Lawrence, C.M.
CitationJournal: J.Virol. / Year: 2004
Title: Crystal structure of F-93 from Sulfolobus spindle-shaped virus 1, a winged-helix DNA binding protein.
Authors: Kraft, P. / Oeckinghaus, A. / Kummel, D. / Gauss, G.H. / Gilmore, J. / Wiedenheft, B. / Young, M. / Lawrence, C.M.
History
DepositionMay 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical 11.0 kDa protein
B: Hypothetical 11.0 kDa protein


Theoretical massNumber of molelcules
Total (without water)23,8112
Polymers23,8112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-19 kcal/mol
Surface area9930 Å2
MethodPISA
2
A: Hypothetical 11.0 kDa protein
B: Hypothetical 11.0 kDa protein

A: Hypothetical 11.0 kDa protein
B: Hypothetical 11.0 kDa protein


Theoretical massNumber of molelcules
Total (without water)47,6224
Polymers47,6224
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_545y+1/4,x-1/4,-z+3/41
Buried area6270 Å2
ΔGint-49 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.493, 120.493, 120.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAASPAA11 - 1911 - 19
21ALAASPBB11 - 1911 - 19
32ALAASNAA24 - 3324 - 33
42ALAASNBB24 - 3324 - 33
53THRGLUAA40 - 5340 - 53
63THRGLUBB40 - 5340 - 53
74GLULYSAA71 - 9171 - 91
84GLULYSBB71 - 9171 - 91
DetailsThe biological assembly is thought to correspond to the dimer of the asymmetric unit.

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Components

#1: Protein Hypothetical 11.0 kDa protein / ORF F-93


Mass: 11905.413 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus virus 1 / Genus: Fusellovirus / Production host: Escherichia coli (E. coli) / References: UniProt: P20222

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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: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 3.25 M NaCl, 120 mM HEPES, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9790, 0.9787, 0.9562
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97871
30.95621
ReflectionResolution: 2.7→20 Å / Num. obs: 7936 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Redundancy: 9.24 % / Rsym value: 0.05 / Net I/σ(I): 41
Reflection shellResolution: 2.7→2.81 Å / Rsym value: 0.167 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.907 / SU B: 13.643 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.491 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25945 401 4.8 %RANDOM
Rwork0.1914 ---
obs0.19448 7936 97.17 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.457 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.317 Å0.491 Å
Luzzati d res low-2.7 Å
Refinement stepCycle: LAST / Resolution: 2.7→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 0 0 1535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221572
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.9652111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2025182
X-RAY DIFFRACTIONr_chiral_restr0.1190.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021167
X-RAY DIFFRACTIONr_nbd_refined0.2550.2779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.240
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3270.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.24
X-RAY DIFFRACTIONr_mcbond_it2.9835916
X-RAY DIFFRACTIONr_mcangle_it4.60261476
X-RAY DIFFRACTIONr_scbond_it4.8196656
X-RAY DIFFRACTIONr_scangle_it6.6427.5635
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
216tight positional0.080.05
229medium positional0.570.5
216tight thermal0.220.5
229medium thermal1.792
LS refinement shellResolution: 2.7→2.771 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 23
Rwork0.277 557
Refinement TLS params.Method: refined / Origin x: 79.7916 Å / Origin y: 60.6764 Å / Origin z: 35.9355 Å
111213212223313233
T0.4123 Å20.123 Å20.0218 Å2-0.4392 Å20.1351 Å2--0.0663 Å2
L6.6315 °2-1.475 °2-4.2961 °2-3.5343 °2-0.5633 °2--6.4668 °2
S-0.1009 Å °0.1736 Å °-0.0181 Å °0.5072 Å °0.1233 Å °0.1963 Å °-0.7312 Å °-0.4417 Å °-0.0225 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B2 - 91
2X-RAY DIFFRACTION1A3 - 96

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