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- PDB-3pov: Crystal structure of a SOX-DNA complex -

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Basic information

Entry
Database: PDB / ID: 3pov
TitleCrystal structure of a SOX-DNA complex
Components
  • DNA (5'-D(*GP*GP*GP*AP*TP*CP*CP*TP*CP*CP*CP*AP*GP*TP*CP*GP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*CP*GP*AP*CP*TP*AP*GP*GP*AP*GP*GP*AP*TP*CP*CP*C)-3')
  • ORF 37
KeywordsDNA BINDING PROTEIN/DNA / Type II restriction endonuclease superfamily / Nuclease / Nucleus/cytoplasm / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


exonuclease activity / endonuclease activity / host cell cytoplasm / host cell nucleus / DNA binding / metal ion binding
Similarity search - Function
Herpesvirus alkaline exonuclease, N-terminal domain / Alphaherpesvirus alkaline exonuclease / Viral alkaline exonuclease / Viral alkaline exonuclease / Restriction endonuclease type II-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / DNA / DNA (> 10) / ORF 37
Similarity search - Component
Biological speciesHuman herpesvirus 8 type M
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBagneris, C. / Barrett, T.E.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Crystal structure of a KSHV-SOX-DNA complex: insights into the molecular mechanisms underlying DNase activity and host shutoff
Authors: Bagneris, C. / Briggs, L.C. / Savva, R. / Ebrahimi, B. / Barrett, T.E.
History
DepositionNov 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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: ORF 37
C: DNA (5'-D(*GP*GP*GP*AP*TP*CP*CP*TP*CP*CP*CP*AP*GP*TP*CP*GP*AP*CP*C)-3')
D: DNA (5'-D(*GP*GP*TP*CP*GP*AP*CP*TP*AP*GP*GP*AP*GP*GP*AP*TP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0326
Polymers66,9373
Non-polymers953
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-23 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.520, 67.660, 174.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ORF 37


Mass: 55299.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 type M / Gene: orf37 / Plasmid: pETM6T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: P88925

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*GP*GP*GP*AP*TP*CP*CP*TP*CP*CP*CP*AP*GP*TP*CP*GP*AP*CP*C)-3')


Mass: 5766.725 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesised by eurogentec
#3: DNA chain DNA (5'-D(*GP*GP*TP*CP*GP*AP*CP*TP*AP*GP*GP*AP*GP*GP*AP*TP*CP*CP*C)-3')


Mass: 5870.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesised by eurogentec

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Non-polymers , 3 types, 128 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 180mM ammonium formate, 19% PEG 3350, pH 7.5, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2009
RadiationMonochromator: channel-cut silicon [111] monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→63.087 Å / Num. all: 22693 / Num. obs: 22693 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 48.58 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.6 / Num. unique all: 755 / % possible all: 99.4

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: protein co-ordinates from entry 3FHD

3fhd


Resolution: 2.5→63.087 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7901 / SU ML: 0.39 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.66 / Phase error: 27.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 1158 5.13 %Random
Rwork0.2065 ---
obs0.2093 22579 97.7 %-
all-22693 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.777 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 349.47 Å2 / Biso mean: 65.9427 Å2 / Biso min: 19.26 Å2
Baniso -1Baniso -2Baniso -3
1--3.191 Å2-0 Å20 Å2
2---17.518 Å2-0 Å2
3---20.7091 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.5→63.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 772 5 125 4373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044432
X-RAY DIFFRACTIONf_angle_d0.766182
X-RAY DIFFRACTIONf_chiral_restr0.045686
X-RAY DIFFRACTIONf_plane_restr0.003658
X-RAY DIFFRACTIONf_dihedral_angle_d21.1321594
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.61390.33791460.27162655280199
2.6139-2.75170.31911550.24962612276798
2.7517-2.92410.32761450.22422674281999
2.9241-3.14980.31681360.21482665280199
3.1498-3.46680.2441280.18892708283698
3.4668-3.96840.22471370.17792687282498
3.9684-4.99940.19711560.16282683283997
4.9994-63.10690.27961550.20352737289294
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)
10.3397-0.3124-0.60272.15680.25071.853-0.3106-0.49650.14980.6142-0.288-1.03290.21160.8978-0.07380.3441-0.07480.02280.57670.01890.83921.8958-3.3525-16.5227
20.4565-0.08410.45191.4253-0.34180.768-0.049-0.0044-0.35940.26760.119-0.25630.20150.022900.2761-0.0229-0.01810.2499-0.05410.29758.5342-16.1409-14.5618
30.1792-0.44080.63560.4024-0.357-0.23220.0869-0.032-0.1819-0.02260.1554-0.4028-0.11670.14810.00010.3871-0.05940.02150.3281-0.0420.41892.67294.727-18.3232
40.2349-0.0927-0.10580.4798-0.3620.1159-0.19090.0431-0.21390.62980.25260.1650.34340.14360.00010.37610.00280.09260.26170.0190.1801-3.70913.7933-5.8476
50.8150.60180.65571.04670.76470.7207-0.15240.12210.158-0.0087-0.0190.5531-0.1810.095700.21980.01730.06750.1620.02210.318-12.696422.2681-15.3526
60.61210.5954-0.88420.6801-1.39522.86840.1850.2510.53150.05660.42230.7251-0.2903-0.47730.52390.36770.012-0.08690.4860.03030.7227-24.612520.6511-27.4382
70.54-0.80490.66951.018-0.41650.4539-0.1265-0.2021-0.29650.28050.34940.64490.1238-0.01610.01370.1867-0.02970.09530.27480.03970.3945-14.499912.2324-13.2631
80.3091-0.33110.7230.2362-0.37980.769-0.0836-0.03030.01790.403-0.07340.0621-0.0050.0799-0.00010.35610.02150.0580.2885-0.00710.2751-3.329721.6675-7.6108
90.11480.03840.20290.3549-0.32210.46480.1259-0.3789-0.4573-0.56040.01550.72710.38730.1693-0.00820.3423-0.0736-0.14190.3451-0.05130.5781-11.8523-5.4802-23.666
100.0443-0.00620.03970.05780.09930.05350.83340.5484-0.6356-0.0915-0.39080.87490.18740.06440.00020.69840.06690.02790.4003-0.16460.5536-0.2277-15.3932-29.3226
110.02210.03150.02580.0335-0.0328-0.005-0.60690.20470.08250.5988-0.28840.7176-0.39580.37450.00040.4141-0.0998-0.14540.28470.20570.55110.533517.807-23.15
120.72540.2738-0.53590.4087-0.07371.36420.08440.9897-0.49230.09240.6640.9775-0.82570.89060.10430.67660.0143-0.41351.07690.15460.6125-7.044619.308-39.3139
130.02590.18030.09270.7382-0.06030.11480.60970.8347-1.00850.8085-0.81190.8692-1.38-0.15690.05960.91950.3276-0.63421.41530.2631.0745-28.973321.9154-52.5552
140.03460.0277-0.05060.06360.00020.07010.32510.4517-0.26120.68120.20120.2176-1.1601-0.3610.00011.0630.3089-0.86071.60890.39362.1498-34.179418.8849-54.1929
15-0.0097-0.0089-0.02360.05910.07240.1462-0.03410.9927-0.56970.3155-0.0686-0.2484-0.18890.98040.18340.4624-0.0418-0.41730.90640.24450.5268-14.870419.7837-41.0301
16-0.02240.0237-0.01630.01950.01340.00150.43140.5722-0.5841-0.384-0.2465-0.5117-0.34360.1312-0.00010.3786-0.18340.02251.9889-0.04170.96835.583118.6253-31.4488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:34)A4 - 34
2X-RAY DIFFRACTION2(chain A and resid 35:127)A35 - 127
3X-RAY DIFFRACTION3(chain A and resid 128:189)A128 - 189
4X-RAY DIFFRACTION4(chain A and resid 190:224)A190 - 224
5X-RAY DIFFRACTION5(chain A and resid 225:307)A225 - 307
6X-RAY DIFFRACTION6(chain A and resid 308:322)A308 - 322
7X-RAY DIFFRACTION7(chain A and resid 323:390)A323 - 390
8X-RAY DIFFRACTION8(chain A and resid 391:443)A391 - 443
9X-RAY DIFFRACTION9(chain A and resid 444:461)A444 - 461
10X-RAY DIFFRACTION10(chain A and resid 462:481)A462 - 481
11X-RAY DIFFRACTION11(chain C and resid 1:4)C1 - 4
12X-RAY DIFFRACTION12(chain C and resid 5:12)C5 - 12
13X-RAY DIFFRACTION13(chain C and resid 13:20)C13 - 20
14X-RAY DIFFRACTION14(chain D and resid 21:26)D21 - 26
15X-RAY DIFFRACTION15(chain D and resid 27:34)D27 - 34
16X-RAY DIFFRACTION16(chain D and resid 35:40)D35 - 40

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