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- PDB-1ab4: 59KDA FRAGMENT OF GYRASE A FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1ab4
Title59KDA FRAGMENT OF GYRASE A FROM E. COLI
ComponentsGYRASE A
KeywordsTOPOISOMERASE / TOPOISOMERASE II / GYRASE / SUPERCOILING DNA
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
Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / Gyrase A; domain 2 - #40 / 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. ...Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / Gyrase A; domain 2 - #40 / 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 / Gyrase A; domain 2 / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA gyrase subunit A / DNA gyrase subunit A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.8 Å
AuthorsCabral, J.H.M. / Maxwell, A. / Liddington, R.C.
Citation
Journal: Nature / Year: 1997
Title: Crystal structure of the breakage-reunion domain of DNA gyrase.
Authors: Cabral, J.H. / Jackson, A.P. / Smith, C.V. / Shikotra, N. / Maxwell, A. / Liddington, R.C.
#1: Journal: Nature / Year: 1996
Title: Structure and Mechanism of DNA Topoisomerase II
Authors: Berger, J.M. / Gamblin, S.J. / Harrison, S.C. / Wang, J.C.
#2: Journal: Nature / Year: 1996
Title: Erratum. Structure and Mechanism of DNA Topoisomerase II
Authors: Berger, J.M. / Gamblin, S.J. / Harrison, S.C. / Wang, J.C.
#3: Journal: Crit.Rev.Biochem.Mol.Biol. / Year: 1991
Title: DNA Gyrase: Structure and Function
Authors: Reece, R.J. / Maxwell, A.
History
DepositionFeb 3, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 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

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Assembly

Deposited unit
A: GYRASE A


Theoretical massNumber of molelcules
Total (without water)55,3811
Polymers55,3811
Non-polymers00
Water27015
1
A: GYRASE A

A: GYRASE A


Theoretical massNumber of molelcules
Total (without water)110,7632
Polymers110,7632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area3570 Å2
ΔGint-18 kcal/mol
Surface area42060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.630, 119.630, 94.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein GYRASE A


Mass: 55381.398 Da / Num. of mol.: 1 / Fragment: 59KDA FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P09097, UniProt: P0AES4*PLUS, EC: 5.99.1.3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTYROSINE 122 IS INVOLVED IN THE TRANSESTERIFICATION REACTION WITH DNA PHOSPHORYL GROUPS.

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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: 3.07 Å3/Da / Density % sol: 60 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLISED FROM 8% PEG 8000, 0.02M NACL 0.1 M TRIS PH8.5.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 %PEG800011
220 mM11NaCl
30.1 MTris-HCl11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 16475 / % possible obs: 100 % / Redundancy: 7 % / Rsym value: 0.047 / Net I/σ(I): 20
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6 % / Mean I/σ(I) obs: 10 / Rsym value: 0.156 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.047

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUPED RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT CORRECTION
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1628 9.9 %RANDOM
Rwork0.226 ---
obs0.226 16367 99.4 %-
Displacement parametersBiso mean: 39.8 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3771 0 0 15 3786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
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
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.418 237 11.5 %
Rwork0.359 1800 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.31
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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