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- PDB-4wub: N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit gr... -

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Basic information

Entry
Database: PDB / ID: 4wub
TitleN-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM KCl condition
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / DNA gyrase / ATPase domain / ATPase activity / GHKL superfamily / monovalent cations
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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 negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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 / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 ...: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Toprim domain profile. / TOPRIM domain / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsHearnshaw, S.J. / Chung, T.T. / Stevenson, C.E.M. / Maxwell, A. / Lawson, D.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The role of monovalent cations in the ATPase reaction of DNA gyrase
Authors: Hearnshaw, S.J. / Chung, T.T. / Stevenson, C.E.M. / Maxwell, A. / Lawson, D.M.
History
DepositionOct 31, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Derived calculations
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
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 B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9446
Polymers43,3161
Non-polymers6285
Water4,486249
1
A: DNA gyrase subunit B
hetero molecules

A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,88812
Polymers86,6322
Non-polymers1,25610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area8270 Å2
ΔGint-97 kcal/mol
Surface area29550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.880, 140.900, 79.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-732-

HOH

21A-749-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA gyrase subunit B


Mass: 43315.766 Da / Num. of mol.: 1 / Fragment: N-terminal 43 kDa fragment, UNP residues 2-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: gyrB, acrB, himB, hisU, nalC, parA, pcbA, b3699, JW5625
Plasmid: pAJ1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P0AES6, EC: 5.99.1.3

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Non-polymers , 6 types, 254 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15-25% PEG 3350, 2 mM MgCl2, 100 mM Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.75→36.74 Å / Num. obs: 50058 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Net I/σ(I): 19.1 / Num. measured all: 298692
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.75-1.85.30.84921942136850.7270.40499.9
7.83-36.745.40.04543.733736260.9970.02198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EI1

1ei1


Resolution: 1.75→36.74 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.451 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 2538 5.1 %RANDOM
Rwork0.1787 47498 --
obs0.1799 -99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.22 Å2 / Biso mean: 35.815 Å2 / Biso min: 21.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2--1.73 Å20 Å2
3----1.14 Å2
Refinement stepCycle: final / Resolution: 1.75→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2923 0 35 257 3215
Biso mean--27.79 41.36 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193038
X-RAY DIFFRACTIONr_bond_other_d0.0010.022837
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9454127
X-RAY DIFFRACTIONr_angle_other_deg0.74436515
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0755390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72524.317139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44515499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.381519
X-RAY DIFFRACTIONr_chiral_restr0.0730.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023545
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02692
X-RAY DIFFRACTIONr_mcbond_it1.1052.1661542
X-RAY DIFFRACTIONr_mcbond_other1.1052.1651541
X-RAY DIFFRACTIONr_mcangle_it1.633.2441926
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 180 -
Rwork0.292 3495 -
all-3675 -
obs--99.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.09920.7373-0.12861.1224-0.04461.1125-0.2008-0.0354-0.3250.06740.0749-0.16760.11770.18220.12580.0840.0310.05230.03760.01420.07517.321822.1768-18.5309
20.90940.33760.3625.07991.10691.08430.01470.13720.1551-0.2707-0.06150.1936-0.20670.02150.04680.08490.0152-0.02220.05430.00280.05879.882748.0956-3.8887
33.5957-1.4914-5.66320.73382.3578.92240.00010.4255-0.07350.0405-0.13430.27570.0485-0.66920.13420.40610.036-0.04330.29950.00210.57091.226161.1362-3.1885
40.29770.24310.09041.96830.32440.7698-0.0380.02860.11430.1067-0.06070.4114-0.1078-0.09620.09870.08330.02-0.02680.0562-0.02310.14733.982250.0871-4.5103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 219
2X-RAY DIFFRACTION2A220 - 299
3X-RAY DIFFRACTION3A300 - 318
4X-RAY DIFFRACTION4A319 - 392

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