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- PDB-4rul: Crystal structure of full-length E.Coli topoisomerase I in comple... -

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Basic information

Entry
Database: PDB / ID: 4rul
TitleCrystal structure of full-length E.Coli topoisomerase I in complex with ssDNA
Components
  • DNA topoisomerase 1Topoisomerase
  • single strand DNA
KeywordsISOMERASE/DNA / TOPOISOMERASE 1A / ISOMERASE-DNA complex
Function / homology
Function and homology information


DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / chromosome / DNA binding / metal ion binding / cytosol
Similarity search - Function
DNA topoisomerase I, zinc ribbon-like, bacterial-type / : / Topoisomerase I zinc-ribbon-like / Topoisomerase I, zinc finger / DNA topoisomerase, type IA, zn finger / Topoisomerase DNA binding C4 zinc finger / DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA / DNA topoisomerase 1, TOPRIM domain / Topoisomerase I, domain 3 ...DNA topoisomerase I, zinc ribbon-like, bacterial-type / : / Topoisomerase I zinc-ribbon-like / Topoisomerase I, zinc finger / DNA topoisomerase, type IA, zn finger / Topoisomerase DNA binding C4 zinc finger / 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
DNA / DNA (> 10) / : / DNA topoisomerase 1
Similarity search - Component
Biological speciesEscherichia coli DH1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTan, K. / Chen, B. / Tse-Dinh, Y.C.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural basis for suppression of hypernegative DNA supercoiling by E. coli topoisomerase I.
Authors: Tan, K. / Zhou, Q. / Cheng, B. / Zhang, Z. / Joachimiak, A. / Tse-Dinh, Y.C.
History
DepositionNov 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2016Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: DNA topoisomerase 1
B: single strand DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,37111
Polymers106,6332
Non-polymers7389
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-75 kcal/mol
Surface area42760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.613, 80.295, 97.475
Angle α, β, γ (deg.)90.00, 91.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / DNA chain , 2 types, 2 molecules AB

#1: Protein DNA topoisomerase 1 / Topoisomerase / DNA topoisomerase I


Mass: 97635.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH1 (bacteria) / Strain: DH1 / Gene: ECDH1ME8569_1213, EcDH1_2375, ESCHERICHIA COLI, topA / Plasmid: pLIC-HK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3)
References: UniProt: C9QXS7, UniProt: P06612*PLUS, DNA topoisomerase
#2: DNA chain single strand DNA


Mass: 8997.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 47 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.15 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.125M ammonium sulfate, 0.1M MES, 1mM zinc sulfate, 19% PEG 5000 monomethyl ether, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97913 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2014 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.9→38 Å / Num. all: 29533 / Num. obs: 29533 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 3.5 % / Biso Wilson estimate: 66.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 23.4
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data reduction
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 3PWT

3pwt


Resolution: 2.9→37.735 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 1492 5.06 %
Rwork0.2095 --
obs0.2119 29508 99.55 %
all-29508 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→37.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6141 252 30 38 6461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036587
X-RAY DIFFRACTIONf_angle_d0.6178997
X-RAY DIFFRACTIONf_dihedral_angle_d13.8292389
X-RAY DIFFRACTIONf_chiral_restr0.041002
X-RAY DIFFRACTIONf_plane_restr0.0031139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.3471220.29432511X-RAY DIFFRACTION99
2.99-3.09680.31671400.26312557X-RAY DIFFRACTION100
3.0968-3.22070.31021430.25662512X-RAY DIFFRACTION100
3.2207-3.36720.34521400.2512577X-RAY DIFFRACTION100
3.3672-3.54460.26351390.22412505X-RAY DIFFRACTION100
3.5446-3.76650.27491260.20942579X-RAY DIFFRACTION100
3.7665-4.0570.25621310.18652559X-RAY DIFFRACTION100
4.057-4.46470.23331200.17522548X-RAY DIFFRACTION100
4.4647-5.10940.19161510.17822553X-RAY DIFFRACTION100
5.1094-6.43210.26031380.21512553X-RAY DIFFRACTION100
6.4321-37.73810.26091420.21272562X-RAY DIFFRACTION97
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)
11.3794-0.1116-0.4211.59950.60311.92540.0646-0.0819-0.06890.028-0.058-0.11580.20160.0372-0.02210.4143-0.0080.02650.22570.10020.557333.817-2.22582.0072
21.4041-0.0765-0.25460.93170.46013.15630.10660.1240.0392-0.1122-0.08910.06990.0237-0.1638-0.02530.34860.0530.04750.37160.04420.62421.77162.4151-4.1169
31.1492-0.256-0.5221.9633-1.36171.8163-0.0047-0.37620.19640.05430.30250.19590.3829-0.3005-0.31480.6282-0.1161-0.11010.9977-0.14130.82542.2399-18.215219.1499
41.1421.1265-0.31651.9245-2.41275.66810.37750.76220.0378-0.34730.0382-0.00390.40881.1922-0.37850.8944-0.1247-0.06721.1397-0.26061.051710.9318-19.473224.6934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:417 )A2 - 417
2X-RAY DIFFRACTION2( CHAIN A AND RESID 418:579 )A418 - 579
3X-RAY DIFFRACTION3( CHAIN A AND RESID 580:862 )A580 - 862
4X-RAY DIFFRACTION4( CHAIN B AND RESID 17:29 )B17 - 29

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