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- PDB-2csb: Crystal structure of Topoisomerase V from Methanopyrus kandleri (... -

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Basic information

Entry
Database: PDB / ID: 2csb
TitleCrystal structure of Topoisomerase V from Methanopyrus kandleri (61 kDa fragment)
ComponentsTopoisomerase V
KeywordsISOMERASE / topoisomerase IB / topoisomerase V / helix-turn-helix / helix-hairpin-helix / HhH motif / three helix bundle / Methanopyrus kandleri
Function / homology
Function and homology information


isomerase activity / DNA repair / DNA 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 / : / : / Topoisomerase V, second (HhH)2 tandem domain / SAM domain-like / Topoisomerase V, HHH domain / 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 - #950 / DNA topoisomerase V, catalytic domain superfamily / : / : / Topoisomerase V, second (HhH)2 tandem domain / SAM domain-like / Topoisomerase V, HHH domain / 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 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsTaneja, B. / Patel, A. / Slesarev, A. / Mondragon, A.
CitationJournal: Embo J. / Year: 2006
Title: Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases
Authors: Taneja, B. / Patel, A. / Slesarev, A. / Mondragon, A.
History
DepositionMay 21, 2005Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Dec 6, 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Topoisomerase V
B: Topoisomerase V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,6873
Polymers120,6632
Non-polymers241
Water9,296516
1
A: Topoisomerase V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3562
Polymers60,3311
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Topoisomerase V


Theoretical massNumber of molelcules
Total (without water)60,3311
Polymers60,3311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.690, 89.770, 189.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 2 / Auth seq-ID: 3 - 266 / Label seq-ID: 3 - 266

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Topoisomerase V / Top61


Mass: 60331.289 Da / Num. of mol.: 2 / Fragment: N-term 61 kDa fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 20094872, UniProt: Q977W1*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3350, Na-cacodylate, MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 1, 2003
RadiationMonochromator: Silicon mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→27.7 Å / Num. all: 53175 / Num. obs: 53175 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rsym value: 0.064 / Net I/σ(I): 9.6
Reflection shellHighest resolution: 2.3 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.262 / % possible all: 94.8

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
SOLVEphasing
SHARPphasing
REFMAC5refinement
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→26.44 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.885 / SU B: 17.051 / SU ML: 0.226 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29227 2687 5.1 %RANDOM
Rwork0.21668 ---
obs0.22046 50430 97.91 %-
all-50430 --
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: 39.487 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8410 0 1 516 8927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228649
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.97611668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92551032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96222.684462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.386151650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.55315125
X-RAY DIFFRACTIONr_chiral_restr0.110.21284
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026569
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.24244
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.25863
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2440
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9461.55373
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33828348
X-RAY DIFFRACTIONr_scbond_it2.33533725
X-RAY DIFFRACTIONr_scangle_it3.6364.53320
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
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
1056tight positional0.10.05
1092medium positional0.560.5
1056tight thermal0.180.5
1092medium thermal1.012
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 201 -
Rwork0.258 3518 -
obs--94.39 %
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)
12.05190.11620.21490.72930.05421.3011-0.0616-0.10980.3074-0.07840.00930.1473-0.0567-0.16680.0523-0.0745-0.0048-0.0327-0.1538-0.0298-0.06950.47570.931164.293
20.72370.1862-0.02170.15230.02630.87070.0049-0.119-0.01610.0721-0.1305-0.072-0.07430.06460.1256-0.022-0.0148-0.0154-0.040.0053-0.104425.22570.599169.779
31.42590.445-0.34161.9634-0.78591.44730.01090.045-0.1340.0120.10590.2592-0.0004-0.053-0.1168-0.0277-0.0029-0.0274-0.0759-0.0531-0.04580.86117.705156.941
41.89420.61581.19041.3802-0.01911.71380.3229-0.3178-0.41670.28520.0469-0.00730.0444-0.1774-0.3698-0.18330.00820.0578-0.10650.09240.0225-17.778111.09174.783
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 2663 - 266
2X-RAY DIFFRACTION2AA296 - 519296 - 519
3X-RAY DIFFRACTION3BB3 - 2663 - 266
4X-RAY DIFFRACTION4BB296 - 519296 - 519

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