- 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
Title
CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM
Components
DNA TOPOISOMERASE I
Keywords
ISOMERASE / 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. / Topoisomerase I; domain 3 / 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 / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / Distorted Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha Similarity search - Domain/homology
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
Resolution: 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
Name
Version
Classification
CNS
0.9
refinement
REFMAC
refinement
X-PLOR
refinement
AMoRE
phasing
DENZO
datareduction
CCP4
(SCALA)
datascaling
Refinement
Resolution: 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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.282
2166
5 %
RANDOM
Rwork
0.229
-
-
-
all
0.234
44947
-
-
obs
0.234
43571
88.3 %
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Displacement parameters
Biso mean: 41.6 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.93 Å2
4.37 Å2
0 Å2
2-
-
0.93 Å2
0 Å2
3-
-
-
-1.86 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.38 Å
0.29 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.33 Å
0.24 Å
Refinement step
Cycle: LAST / Resolution: 2.15→14.97 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3939
0
1
380
4320
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
c_bond_d
0.008
X-RAY DIFFRACTION
c_bond_d_na
X-RAY DIFFRACTION
c_bond_d_prot
X-RAY DIFFRACTION
c_angle_d
X-RAY DIFFRACTION
c_angle_d_na
X-RAY DIFFRACTION
c_angle_d_prot
X-RAY DIFFRACTION
c_angle_deg
1.4
X-RAY DIFFRACTION
c_angle_deg_na
X-RAY DIFFRACTION
c_angle_deg_prot
X-RAY DIFFRACTION
c_dihedral_angle_d
23.7
X-RAY DIFFRACTION
c_dihedral_angle_d_na
X-RAY DIFFRACTION
c_dihedral_angle_d_prot
X-RAY DIFFRACTION
c_improper_angle_d
0.88
X-RAY DIFFRACTION
c_improper_angle_d_na
X-RAY DIFFRACTION
c_improper_angle_d_prot
X-RAY DIFFRACTION
c_mcbond_it
1.09
2
X-RAY DIFFRACTION
c_mcangle_it
1.89
3
X-RAY DIFFRACTION
c_scbond_it
1.16
2
X-RAY DIFFRACTION
c_scangle_it
2
3
LS refinement shell
Resolution: 2.15→2.23 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
Rfactor
Num. reflection
% reflection
Rfree
0.382
178
4.6 %
Rwork
0.288
3732
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obs
-
-
81.2 %
Xplor file
Refine-ID
Serial no
Param file
Topol file
X-RAY DIFFRACTION
1
PROTEIN_REP.PA
PROTEIN.TOP
X-RAY DIFFRACTION
2
WATER_REP.PARA
WATER.TOP
X-RAY DIFFRACTION
3
ION.PARAM
ION.TOP
Software
*PLUS
Name: 'REFMAC, XPLOR AND CNS 0.9' / Classification: refinement
Refine LS restraints
*PLUS
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
p_bond_d
X-RAY DIFFRACTION
p_angle_d
X-RAY DIFFRACTION
p_angle_deg
X-RAY DIFFRACTION
p_dihedral_angle_d
X-RAY DIFFRACTION
p_dihedral_angle_deg
23.7
X-RAY DIFFRACTION
p_improper_angle_d
X-RAY DIFFRACTION
p_improper_angle_deg
0.88
X-RAY DIFFRACTION
p_mcbond_it
X-RAY DIFFRACTION
p_scbond_it
X-RAY DIFFRACTION
p_mcangle_it
X-RAY DIFFRACTION
p_scangle_it
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