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- PDB-1cyy: CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOME... -

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Basic information

Entry
Database: PDB / ID: 1cyy
TitleCRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM
ComponentsDNA TOPOISOMERASE ITopoisomerase
KeywordsISOMERASE / DNA TOPOISOMERASE / DECATENATING ENZYME
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 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å
AuthorsFeinberg, H. / Lima, C. / Mondragon, A.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Conformational changes in E. coli DNA topoisomerase I.
Authors: Feinberg, H. / Lima, C.D. / Mondragon, A.
History
DepositionAug 31, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: DNA TOPOISOMERASE I
B: DNA TOPOISOMERASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3853
Polymers59,3192
Non-polymers651
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-19 kcal/mol
Surface area24960 Å2
MethodPISA
2
A: DNA TOPOISOMERASE I
B: DNA TOPOISOMERASE I
hetero molecules

A: DNA TOPOISOMERASE I
B: DNA TOPOISOMERASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7696
Polymers118,6384
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+2/31
Buried area9990 Å2
ΔGint-94 kcal/mol
Surface area45770 Å2
MethodPISA
3
A: DNA TOPOISOMERASE I
hetero molecules

B: DNA TOPOISOMERASE I


Theoretical massNumber of molelcules
Total (without water)59,3853
Polymers59,3192
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+2/31
Buried area840 Å2
ΔGint-29 kcal/mol
Surface area27040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.850, 113.850, 233.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein DNA TOPOISOMERASE I / Topoisomerase


Mass: 29659.596 Da / Num. of mol.: 2 / Fragment: 30 KDA FRAGMENT COMPRISING DOMAINS II AND III
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P06612, DNA topoisomerase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 380 / 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: 3.69 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M AMMONIUM SULFATE, 100MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.002
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.002 Å / Relative weight: 1
ReflectionResolution: 2.15→29 Å / Num. all: 259275 / Num. obs: 45125 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.5
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.261 / % possible all: 85.8
Reflection
*PLUS
Num. measured all: 259275
Reflection shell
*PLUS
% possible obs: 85.8 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
REFMACrefinement
X-PLORrefinement
AMoREphasing
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.15→14.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 330269769.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: R. A. ENGH AND R. HUBER, ACTA CRYST. SECT. A., 1991
Details: MOST OF THE REFINEMENT DONE WITH REFMAC. SOLVENT CORRECTION WITH XPLOR. FINAL REFINEMENT WITH CNS 0.9
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2166 5 %RANDOM
Rwork0.229 ---
all0.234 44947 --
obs0.234 43571 88.3 %-
Displacement parametersBiso mean: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å24.37 Å20 Å2
2--0.93 Å20 Å2
3----1.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.15→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 1 380 4320
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.092
X-RAY DIFFRACTIONc_mcangle_it1.893
X-RAY DIFFRACTIONc_scbond_it1.162
X-RAY DIFFRACTIONc_scangle_it23
LS refinement shellResolution: 2.15→2.23 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.382 178 4.6 %
Rwork0.288 3732 -
obs--81.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: 'REFMAC, XPLOR AND CNS 0.9' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg23.7
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg0.88
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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