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- PDB-2gaj: Structure of Full Length Topoisomerase I from Thermotoga maritima... -

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Basic information

Entry
Database: PDB / ID: 2gaj
TitleStructure of Full Length Topoisomerase I from Thermotoga maritima in monoclinic crystal form
ComponentsDNA topoisomerase ITopoisomerase
KeywordsISOMERASE / Topoisomerase / Zinc ribbon
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / DNA binding / metal ion binding
Similarity search - Function
DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA / DNA topoisomerase 1, TOPRIM domain / Topoisomerase I, domain 3 / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / DNA topoisomerase, type IA ...DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA / DNA topoisomerase 1, TOPRIM domain / Topoisomerase I, domain 3 / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / Topoisomerase I; domain 3 / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / Distorted Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHansen, G.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Full Length Topoisomerase I from Thermotoga maritima
Authors: Hansen, G. / Harrenga, A. / Wieland, B. / Schomburg, D. / Reinemer, P.
History
DepositionMar 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / 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
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: DNA topoisomerase I
B: DNA topoisomerase I


Theoretical massNumber of molelcules
Total (without water)145,6142
Polymers145,6142
Non-polymers00
Water15,799877
1
A: DNA topoisomerase I


Theoretical massNumber of molelcules
Total (without water)72,8071
Polymers72,8071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA topoisomerase I


Theoretical massNumber of molelcules
Total (without water)72,8071
Polymers72,8071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.049, 142.714, 127.638
Angle α, β, γ (deg.)90.00, 90.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA topoisomerase I / Topoisomerase / Omega-protein / Relaxing enzyme / Untwisting enzyme / Swivelase


Mass: 72806.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: topA / Plasmid: pET28a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46799, DNA topoisomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 877 / 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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 34 % Jeffamine M-600, 100 mM MES/NaOH, 64 mM Sodium Citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.2815 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2815 Å / Relative weight: 1
ReflectionResolution: 1.95→45 Å / Num. all: 116615 / Num. obs: 116615 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.2
Reflection shellResolution: 1.95→2.05 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GAI

2gai


Resolution: 1.95→15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.601 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.246 5837 5 %RANDOM
Rwork0.195 ---
all0.197 116577 --
obs0.197 110740 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.845 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å2-0.47 Å2
2--0.22 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9428 0 0 877 10305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229602
X-RAY DIFFRACTIONr_bond_other_d0.0010.028934
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.97712890
X-RAY DIFFRACTIONr_angle_other_deg1.082320882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg651158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21723.779434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.918151902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9011572
X-RAY DIFFRACTIONr_chiral_restr0.1170.21418
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210394
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021958
X-RAY DIFFRACTIONr_nbd_refined0.2030.21811
X-RAY DIFFRACTIONr_nbd_other0.1790.28767
X-RAY DIFFRACTIONr_nbtor_refined0.1790.24581
X-RAY DIFFRACTIONr_nbtor_other0.0850.25776
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2706
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.231
X-RAY DIFFRACTIONr_mcbond_it1.4351.57544
X-RAY DIFFRACTIONr_mcbond_other0.2651.52354
X-RAY DIFFRACTIONr_mcangle_it1.56929388
X-RAY DIFFRACTIONr_scbond_it2.91934514
X-RAY DIFFRACTIONr_scangle_it4.2824.53502
LS refinement shellHighest resolution: 1.95 Å / Num. reflection Rwork: 8003 / Total num. of bins used: 20
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)
10.4572-0.02530.13830.66810.53531.6666-0.00920.07870.0697-0.10530.00030.0137-0.1308-0.04380.0089-0.1932-0.01430.025-0.11340.0261-0.09442.955571.748567.5442
20.45210.03560.07890.6671-0.43831.4088-0.0122-0.06790.06350.09020.013-0.0306-0.1160.0162-0.0007-0.20080.0190.022-0.131-0.0245-0.1-13.439971.7349123.071
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 7 - 601 / Label seq-ID: 7 - 601

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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