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- PDB-1wp5: Crystal structure of the C-terminal domain of DNA topoisomerase IV -

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Basic information

Entry
Database: PDB / ID: 1wp5
TitleCrystal structure of the C-terminal domain of DNA topoisomerase IV
Componentstopoisomerase IV
KeywordsISOMERASE / broken beta-propeller / hairpin-invaded beta-propeller / six-bladed beta-propeller
Function / homologyDNA gyrase/topoisomerase IV, subunit A, C-terminal / 6 Propeller / Neuraminidase / Mainly Beta
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.79 Å
AuthorsHsieh, T.-J. / Farh, L. / Huang, W.M. / Chan, N.-L.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure of the topoisomerase IV C-terminal domain: a broken beta-propeller implies a role as geometry facilitator in catalysis
Authors: Hsieh, T.-J. / Farh, L. / Huang, W.M. / Chan, N.-L.
History
DepositionAug 30, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: topoisomerase IV


Theoretical massNumber of molelcules
Total (without water)37,0111
Polymers37,0111
Non-polymers00
Water6,792377
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.211, 83.211, 44.999
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein topoisomerase IV


Mass: 37010.914 Da / Num. of mol.: 1 / Fragment: Topo IV C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: ParC / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: Isomerases; Other isomerases; Sole sub-subclass for isomerases that do not belong in the other subclasses
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: magnesium acetate, sodium cacodylate, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.95370, 0.97994, 0.97966
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2003
RadiationMonochromator: Si 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.979941
30.979661
ReflectionResolution: 1.79→23.3 Å / Num. all: 32512 / Num. obs: 30204 / % possible obs: 92.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 22.1 Å2 / Rsym value: 0.096
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.2 % / Num. unique all: 1906 / Rsym value: 0.224 / % possible all: 70.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.79→23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.475 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.123 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21381 1548 5.1 %RANDOM
Rwork0.1599 ---
all0.16262 32512 --
obs0.16262 29086 93.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.942 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.79→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 0 377 2952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0212619
X-RAY DIFFRACTIONr_bond_other_d0.0020.022400
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.9493534
X-RAY DIFFRACTIONr_angle_other_deg0.9135588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8435322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1190.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022890
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02519
X-RAY DIFFRACTIONr_nbd_refined0.2240.2479
X-RAY DIFFRACTIONr_nbd_other0.2580.22931
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3350.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3780.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2781.51600
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.28422589
X-RAY DIFFRACTIONr_scbond_it3.39731019
X-RAY DIFFRACTIONr_scangle_it5.434.5945
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.793→1.84 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.236 84
Rwork0.175 1588

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