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- PDB-4gfj: Crystal structure of Topo-78, an N-terminal 78kDa fragment of top... -

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Basic information

Entry
Database: PDB / ID: 4gfj
TitleCrystal structure of Topo-78, an N-terminal 78kDa fragment of topoisomerase V
ComponentsTopoisomerase V
KeywordsISOMERASE / helix-hairpin-helix / DNA repair enzyme / topoisomerase / DNA binding
Function / homology
Function and homology information


isomerase activity / DNA helicase activity / DNA recombination / DNA repair / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #950 / DNA topoisomerase V, catalytic domain superfamily / Bacterial DNA recombination protein RuvA / Winged helix-turn-helix DNA-binding / RuvA domain 2-like / Helix-hairpin-helix domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #950 / DNA topoisomerase V, catalytic domain superfamily / Bacterial DNA recombination protein RuvA / Winged helix-turn-helix DNA-binding / RuvA domain 2-like / Helix-hairpin-helix domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Helix non-globular / Special / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Biological speciesMethanopyrus kandleri AV19 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsRajan, R. / Prasad, R. / Taneja, B. / Wilson, S.H. / Mondragon, A.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Identification of one of the apurinic/apyrimidinic lyase active sites of topoisomerase V by structural and functional studies.
Authors: Rajan, R. / Prasad, R. / Taneja, B. / Wilson, S.H. / Mondragon, A.
History
DepositionAug 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Topoisomerase V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0185
Polymers78,6761
Non-polymers3424
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.634, 161.634, 58.227
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Topoisomerase V /


Mass: 78676.336 Da / Num. of mol.: 1 / Fragment: UNP residues 1-685
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri AV19 (archaea) / Strain: AV19 / Gene: MK1436, Topoisomerase V / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F1SVL0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM HEPES pH 7, 0.1 M KCl, 0.01 M MgCl2, and 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.91→29.1 Å / Num. obs: 19283 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.076 / Net I/σ(I): 20.6
Reflection shellResolution: 2.91→3.04 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2264 / Rsym value: 0.519 / % possible all: 96.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CSB

2csb


Resolution: 2.91→29.1 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.897 / SU B: 35.583 / SU ML: 0.312 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 989 5.1 %RANDOM
Rwork0.20141 ---
all0.20473 19283 --
obs0.20473 18292 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.398 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å2-1.11 Å20 Å2
2---2.21 Å20 Å2
3---3.32 Å2
Refinement stepCycle: LAST / Resolution: 2.91→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4940 0 19 4 4963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225057
X-RAY DIFFRACTIONr_bond_other_d0.0010.023650
X-RAY DIFFRACTIONr_angle_refined_deg1.0351.9946805
X-RAY DIFFRACTIONr_angle_other_deg0.81738794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4345613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61422.874261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22615953
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2471568
X-RAY DIFFRACTIONr_chiral_restr0.0560.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025604
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021065
X-RAY DIFFRACTIONr_mcbond_it0.2821.53045
X-RAY DIFFRACTIONr_mcbond_other0.0391.51239
X-RAY DIFFRACTIONr_mcangle_it0.55524903
X-RAY DIFFRACTIONr_scbond_it1.08632012
X-RAY DIFFRACTIONr_scangle_it1.5844.51902
LS refinement shellResolution: 2.91→2.984 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 58 -
Rwork0.287 1263 -
obs-1263 94.22 %
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)
13.67550.5804-0.22744.32710.08341.3098-0.04050.2137-0.12490.06430.1065-0.0195-0.087-0.1363-0.06610.17040.0249-0.03650.20220.00650.12833.9923-55.6589-3.1772
28.20941.0872-0.36811.95130.52061.2574-0.08460.6317-0.5315-0.1430.09440.0081-0.0845-0.1204-0.00980.13140.018-0.06520.22770.02180.130926.2595-61.0863-7.922
316.59098.63570.66848.0455-0.07394.34010.7178-0.8679-0.18330.8022-0.29210.17020.0987-0.5027-0.42560.4551-0.2273-0.04260.23340.09060.065333.3112-48.852118.8336
45.70652.19950.70514.67753.10412.89780.324-0.22110.0830.1365-0.0696-0.2316-0.06570.0972-0.25440.3107-0.1218-0.08620.1338-0.01750.255951.3363-36.42017.1805
52.677-2.40410.71515.1961-0.67810.19980.23450.23160.12230.1765-0.2078-0.2930.07540.1016-0.02670.18990.0262-0.11770.4195-0.17690.366775.7633-69.8223-2.9358
65.0475-2.3883-0.398311.9514-1.571112.3448-0.50470.0697-0.9060.73280.26630.39350.8598-0.63040.23840.465-0.1876-0.24310.21680.01720.85287.7556-107.747213.5425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 217
2X-RAY DIFFRACTION2A218 - 286
3X-RAY DIFFRACTION3A287 - 358
4X-RAY DIFFRACTION4A359 - 411
5X-RAY DIFFRACTION5A412 - 577
6X-RAY DIFFRACTION6A578 - 612

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