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- PDB-4lid: A100, A DNA binding scaffold from Sulfolobus spindle-shape virus 1 -

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Basic information

Entry
Database: PDB / ID: 4lid
TitleA100, A DNA binding scaffold from Sulfolobus spindle-shape virus 1
ComponentsA-100
KeywordsVIRAL PROTEIN / Hyperthermophilic viral protein / SSV1 / Sulfolobus spindle-shape virus 1 / Archaea / A100 / DNA binding scaffold / A DNA binding scaffold
Function / homologyProtein of unknown function DUF5517 / Family of unknown function (DUF5517) / Uncharacterized protein A-100
Function and homology information
Biological speciesSulfolobus spindle-shaped virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsEilers, B.J. / Wagner, C. / Thomas, M.M. / Lawrence, C.M. / Young, M.J.
CitationJournal: To be Published
Title: A100, A DNA binding scaffold from Sulfolobus spindle-shape virus 1
Authors: Eilers, B.J. / Wagner, C. / Thomas, M.M. / Lawrence, C.M. / Young, M.J.
History
DepositionJul 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: A-100
B: A-100


Theoretical massNumber of molelcules
Total (without water)25,3932
Polymers25,3932
Non-polymers00
Water00
1
A: A-100
B: A-100
x 6


Theoretical massNumber of molelcules
Total (without water)152,35812
Polymers152,35812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area29840 Å2
ΔGint-180 kcal/mol
Surface area49380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.999, 152.999, 61.727
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.997449, 0.024832, 0.066928), (0.022809, -0.999264, 0.030831), (0.067645, -0.029226, -0.997281)-1.79538, 86.53544, 27.88598
DetailsThe biological assembly is a dodecamer generated from the dimer in the asymmetric unit by the operations: x,y,z ; -y+1,-x+1,-z+1/2 ; -y+1,x-y,z ; x,x-y,-z+1/2 ; -x+y+1,-x+1,z ; and -x+y+1,y,-z+1/2 REMARK 350 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA v1.47 [21/3/2013] REMARK 350 TOTAL BURIED SURFACE AREA: 29840 ANGSTROM**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 49380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -180 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.500000 -0.866025 0.000000 76.49950 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 132.50102 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 30.86350 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 152.99900 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 30.86350 REMARK 350 BIOMT1 5 -0.500000 0.866025 0.000000 76.49950 REMARK 350 BIOMT2 5 -0.866025 -0.500000 0.000000 132.50102 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 152.99900 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 30.86350

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Components

#1: Protein A-100


Mass: 12696.460 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus spindle-shaped virus 1 / Gene: a100 / Plasmid: pDest14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P20194

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.1170.05
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2961vapor diffusion, hanging drop5.610mg/ml A100, 0.6-0.9M Ammonium dihydrogen phosphate, 20-30% Glycerol, 0.7M MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K
2962vapor diffusion, hanging drop5.610mg/ml selenomethionine incorporated A100,0.6-0.9M Ammonium dihydrogen phosphate, 20-30% Glycerol, 0.7M MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 102.5 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2013 / Details: K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→38.25 Å / Num. all: 8956 / Num. obs: 8953 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 12.5 % / Biso Wilson estimate: 94.1 Å2 / Rmerge(I) obs: 0.014 / Rsym value: 0.047 / Net I/σ(I): 7.93
Reflection shellResolution: 3→3.16 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1263 / Rsym value: 0.2 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
REFMAC5.7.0029refinement
autoXDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3→21 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 29.633 / SU ML: 0.243 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.525 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25062 423 4.7 %RANDOM
Rwork0.23707 ---
all0.2857 8957 --
obs0.23767 8488 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 122.806 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.25 Å2-0 Å2
2--0.25 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 3→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 0 0 1438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191455
X-RAY DIFFRACTIONr_bond_other_d0.0010.021454
X-RAY DIFFRACTIONr_angle_refined_deg1.74321953
X-RAY DIFFRACTIONr_angle_other_deg2.9633358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51626.13375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3215302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.045155
X-RAY DIFFRACTIONr_chiral_restr0.0830.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021587
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02302
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 36 -
Rwork0.312 591 -
obs--100 %
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)
19.50961.4825-1.04923.1863-0.237221.74270.00730.2676-0.1459-0.04780.09940.059-0.2823-0.3504-0.10670.37450.1139-0.01740.4028-0.08010.431231.776646.320823.6143
212.9715-2.7303-12.99411.80036.574614.4056-0.36643.5838-0.0889-1.45670.3981-0.2679-0.2266-3.4828-0.03161.0749-0.00920.02742.2635-0.11570.319335.645847.22971.669
38.42120.0379-4.68569.2641.512310.6814-0.47472.3109-0.2257-1.26210.3627-0.4117-0.4015-1.2290.11190.9156-0.14850.04131.4507-0.05280.276942.08249.24745.5185
410.87014.9203-0.049411.57434.09496.113-0.28030.64820.4684-0.02010.02780.0822-0.3145-0.50070.25250.46520.04430.0340.55050.06390.224445.311152.429914.9975
514.52840.39816.72858.53922.988721.77250.92321.2178-0.3192-0.0159-1.44261.14041.40330.37040.51940.6957-0.2794-0.02661.4214-0.73020.685532.760738.91543.3526
66.62230.8651-1.38725.88050.49417.5065-0.4751-0.5936-0.25630.87330.3045-0.0909-0.29750.52860.17060.40350.17690.05560.43570.03380.403635.284443.501130.5199
714.64994.576412.04458.09815.928228.9417-0.42880.6432-1.55640.04580.54860.70150.1851-0.4947-0.11970.2760.04340.18620.3486-0.11680.592733.754636.565422.0683
83.7979-1.64662.661710.86013.83015.3979-0.28180.3634-0.6882-0.5170.7116-1.2179-0.05160.7124-0.42980.4012-0.01420.41650.4438-0.21760.967950.513236.518216.527
91.84460.09341.327840.53682.63911.20090.2015-0.3817-0.9589-1.75990.09931.06230.0619-0.5568-0.30080.864-0.24790.3591.0774-0.67321.40741.061728.028611.4994
1013.14080.5082-4.81896.4831.81874.7259-0.52780.1359-0.49020.16430.4404-0.3889-0.18540.11440.08740.41220.03960.03420.4397-0.00460.359941.704244.007520.9118
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 23
2X-RAY DIFFRACTION2A24 - 41
3X-RAY DIFFRACTION3A42 - 61
4X-RAY DIFFRACTION4A62 - 100
5X-RAY DIFFRACTION5B15 - 19
6X-RAY DIFFRACTION6B20 - 33
7X-RAY DIFFRACTION7B34 - 52
8X-RAY DIFFRACTION8B53 - 76
9X-RAY DIFFRACTION9B77 - 85
10X-RAY DIFFRACTION10B86 - 100

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