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- PDB-1vcc: AMINO TERMINAL 9KDA DOMAIN OF VACCINIA VIRUS DNA TOPOISOMERASE I ... -

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Basic information

Entry
Database: PDB / ID: 1vcc
TitleAMINO TERMINAL 9KDA DOMAIN OF VACCINIA VIRUS DNA TOPOISOMERASE I RESIDUES 1-77, EXPERIMENTAL ELECTRON DENSITY FOR RESIDUES 1-77
ComponentsDNA TOPOISOMERASE I
KeywordsDNA BINDING
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / virion component / DNA binding
Similarity search - Function
DNA topoisomerase I, N-terminal, viral / Viral DNA topoisomerase I, N-terminal / Viral Topoisomerase I / DNA topoisomerase I domain / DNA topoisomerase I, N-terminal / DNA topoisomerase I, active site / Topoisomerase (Topo) IB-type active site signature. / DNA topoisomerase I / DNA topoisomerase I, catalytic core, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type ...DNA topoisomerase I, N-terminal, viral / Viral DNA topoisomerase I, N-terminal / Viral Topoisomerase I / DNA topoisomerase I domain / DNA topoisomerase I, N-terminal / DNA topoisomerase I, active site / Topoisomerase (Topo) IB-type active site signature. / DNA topoisomerase I / DNA topoisomerase I, catalytic core, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type / Eukaryotic DNA topoisomerase I, catalytic core / Topoisomerase (Topo) IB-type catalytic domain profile. / DNA breaking-rejoining enzyme, catalytic core / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA topoisomerase 1B
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsSharma, A. / Hanai, R. / Mondragon, A.
CitationJournal: Structure / Year: 1994
Title: Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 A resolution.
Authors: Sharma, A. / Hanai, R. / Mondragon, A.
History
DepositionOct 2, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA TOPOISOMERASE I


Theoretical massNumber of molelcules
Total (without water)9,0661
Polymers9,0661
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.460, 42.510, 60.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA TOPOISOMERASE I


Mass: 9066.254 Da / Num. of mol.: 1 / Fragment: AMINO TERMINAL 9KDA, RESIDUES 1 - 77
Source method: isolated from a genetically manipulated source
Details: DOMAIN GENERATED BY MILD PROTEOLYSIS OF THE INTACT 36KDA VACCINIA VIRUS DNA TOPOISOMERASE I, A MEMBER OF THE EUKARYOTIC-LIKE TYPE I DNA TOPOISOMERASES
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Strain: WR / Description: ACTIVE FORM / Production host: Escherichia coli (E. coli) / References: UniProt: P68698, EC: 5.99.1.2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMTris-HCl1reservoir
20.2 Msodium acetate1reservoir
330 %PEG33001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.59 Å / Lowest resolution: 20 Å / Num. obs: 9781 / Num. measured all: 47905 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
Num. unique obs: 799 / Num. measured obs: 3643 / Rmerge(I) obs: 0.205

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.6→5 Å / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.218 / Rfactor obs: 0.218 / σ(F): 2
Details: THE ELECTRON DENSITY USING EXPERIMENTAL PHASES WAS UNAMBIGUOUS THROUGHOUT RESIDUES 1 - 77; THE MODEL WAS REFINED AGAINST DATA COLLECTED AT ROOM TEMPERATURE (5 - 1.9 ANGSTROMS), AND ...Details: THE ELECTRON DENSITY USING EXPERIMENTAL PHASES WAS UNAMBIGUOUS THROUGHOUT RESIDUES 1 - 77; THE MODEL WAS REFINED AGAINST DATA COLLECTED AT ROOM TEMPERATURE (5 - 1.9 ANGSTROMS), AND SUBSEQUENTLY AGAINST CRYO-COOLED DATA COLLECTED AT THE SYNCHROTRON SOURCE IN PHOTON FACTORY, TSUKUBA, JAPAN IN THE RESOLUTION RANGE OF 5 - 1.6 ANGSTROMS.
Refinement stepCycle: LAST / Resolution: 1.6→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms640 0 0 62 702
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.51
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.73 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.267 / Rfactor obs: 0.3

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