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- PDB-1zi0: A Superhelical Spiral in Escherichia coli DNA Gyrase A C-terminal... -

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Basic information

Entry
Database: PDB / ID: 1zi0
TitleA Superhelical Spiral in Escherichia coli DNA Gyrase A C-terminal Domain Imparts Unidirectional Supercoiling Bias
ComponentsDNA gyrase subunit A
KeywordsISOMERASE / DNA BINDING PROTEIN / beta pinwheel / gyrase / topoisomerase / spiralling beta pinwheel / DNA wrapping
Function / homology
Function and homology information


DNA gyrase complex / negative regulation of DNA-templated DNA replication / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome ...DNA gyrase complex / negative regulation of DNA-templated DNA replication / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / DNA binding / ATP binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase, subunit A / 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 gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase, subunit A / 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 / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
DNA gyrase subunit A / DNA gyrase subunit A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsRuthenburg, A.J. / Graybosch, D.M. / Huetsch, J.C. / Verdine, G.L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias
Authors: Ruthenburg, A.J. / Graybosch, D.M. / Huetsch, J.C. / Verdine, G.L.
History
DepositionApr 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit A
B: DNA gyrase subunit A


Theoretical massNumber of molelcules
Total (without water)67,0252
Polymers67,0252
Non-polymers00
Water2,774154
1
A: DNA gyrase subunit A


Theoretical massNumber of molelcules
Total (without water)33,5121
Polymers33,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit A


Theoretical massNumber of molelcules
Total (without water)33,5121
Polymers33,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.216, 121.432, 177.957
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222

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Components

#1: Protein DNA gyrase subunit A / / E.C.5.99.1.3


Mass: 33512.312 Da / Num. of mol.: 2 / Fragment: C-terminal domain / Mutation: R562C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gyrA, hisW, nalA, parD / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) PlysS
References: UniProt: P09097, UniProt: P0AES4*PLUS, EC: 5.99.1.3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 4.5 Å3/Da / Density % sol: 72.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris, PEG 1500, NaCl, Sodium Phosphate, EDTA, Beta-Mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.936
SYNCHROTRONNSLS X4A20.9739, 0.9786, 0.9791, 0.9795
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJan 20, 2003
ADSC QUANTUM 42CCDMar 7, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Bent triangular asymmetric cut Si(111) monochromater and Rh-coated Si mirrorSINGLE WAVELENGTHMx-ray1
2KOHZU double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9361
20.97391
30.97861
40.97911
50.97951
ReflectionResolution: 2.6→50 Å / Num. all: 34296 / Num. obs: 32428 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 39.3 Å2 / Rsym value: 0.068
Reflection shellResolution: 2.6→2.72 Å / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→39.3 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 381578.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2282 7 %RANDOM
Rwork0.227 ---
all-34296 --
obs-32428 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 86.2809 Å2 / ksol: 0.308562 e/Å3
Displacement parametersBiso mean: 63.2 Å2
Baniso -1Baniso -2Baniso -3
1-22.38 Å20 Å20 Å2
2---2.28 Å20 Å2
3----20.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4169 0 0 154 4323
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 388 7.7 %
Rwork0.309 4683 -
obs-4331 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3water_rep.param

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