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- PDB-1zvt: Structure of the E. coli ParC C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 1zvt
TitleStructure of the E. coli ParC C-terminal domain
ComponentsTopoisomerase IV subunit A
KeywordsISOMERASE / beta-pinwheel / ATPase / supercoiling / decatenation / DNA binding / DNA topology
Function / homology
Function and homology information


plasmid partitioning / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / sister chromatid cohesion / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change / chromosome segregation / chromosome / DNA binding ...plasmid partitioning / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / sister chromatid cohesion / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
DNA topoisomerase IV, subunit A, Gram-negative / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA-like domain superfamily
Similarity search - Domain/homology
DNA topoisomerase 4 subunit A / DNA topoisomerase 4 subunit A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsCorbett, K.D. / Schoeffler, A.J. / Thomsen, N.D. / Berger, J.M.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The Structural Basis for Substrate Specificity in DNA Topoisomerase IV.
Authors: Corbett, K.D. / Schoeffler, A.J. / Thomsen, N.D. / Berger, J.M.
History
DepositionJun 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 29, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Topoisomerase IV subunit A
B: Topoisomerase IV subunit A


Theoretical massNumber of molelcules
Total (without water)55,2032
Polymers55,2032
Non-polymers00
Water6,846380
1
A: Topoisomerase IV subunit A


Theoretical massNumber of molelcules
Total (without water)27,6021
Polymers27,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Topoisomerase IV subunit A


Theoretical massNumber of molelcules
Total (without water)27,6021
Polymers27,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.908, 50.494, 72.759
Angle α, β, γ (deg.)86.11, 86.90, 70.57
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Topoisomerase IV subunit A /


Mass: 27601.652 Da / Num. of mol.: 2 / Fragment: CTD (residues 497-752)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: parC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P20082, UniProt: P0AFI2*PLUS, EC: 5.99.1.-
#2: 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: 2.52 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: HEPES, NaCl, Na acetate, NH4 acetate, PEG-4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1271, 0.9796, 1.0199
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 3, 2004
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.12711
20.97961
31.01991
ReflectionResolution: 1.7→30 Å / Num. all: 57955 / Num. obs: 57955 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.066 / Net I/σ(I): 22
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 5659 / Rsym value: 0.257 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.769 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21548 2937 5.1 %RANDOM
Rwork0.1835 ---
all0.18509 54999 --
obs0.18509 54999 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.165 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å2-0.02 Å20.53 Å2
2--0.22 Å2-0.84 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3705 0 0 380 4085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223767
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9955095
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4055488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19723.973146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56915674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3711530
X-RAY DIFFRACTIONr_chiral_restr0.0920.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022796
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21603
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22539
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2300
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.031.52517
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51823934
X-RAY DIFFRACTIONr_scbond_it2.67631379
X-RAY DIFFRACTIONr_scangle_it4.2744.51161
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 228 -
Rwork0.206 3859 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 2.0715 Å / Origin y: 3.9856 Å / Origin z: 21.1666 Å
111213212223313233
T-0.0768 Å2-0.004 Å20.0113 Å2--0.0178 Å2-0.0035 Å2--0.0029 Å2
L0.0505 °2-0.018 °20.1388 °2-0.2649 °2-0.0979 °2--0.976 °2
S0.0016 Å °-0.0114 Å °0.0123 Å °0.0037 Å °0.0087 Å °0.0083 Å °0.0073 Å °-0.017 Å °-0.0103 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA497 - 7421 - 246
2X-RAY DIFFRACTION1BB497 - 7421 - 246

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