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- PDB-1kij: Crystal structure of the 43K ATPase domain of Thermus thermophilu... -

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Basic information

Entry
Database: PDB / ID: 1kij
TitleCrystal structure of the 43K ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin
ComponentsDNA GYRASE SUBUNIT B
KeywordsISOMERASE / topoisomerase / gyrase B-coumarin complex
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
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. ...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
FORMIC ACID / NOVOBIOCIN / DNA gyrase subunit B / DNA gyrase subunit B
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLamour, V. / Hoermann, L. / Jeltsch, J.-M. / Oudet, P. / Moras, D.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: An open conformation of the Thermus thermophilus gyrase B ATP-binding domain.
Authors: Lamour, V. / Hoermann, L. / Jeltsch, J.M. / Oudet, P. / Moras, D.
History
DepositionDec 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jun 1, 2016Group: Source and taxonomy
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA GYRASE SUBUNIT B
B: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7606
Polymers85,4432
Non-polymers1,3174
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-10 kcal/mol
Surface area33050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.880, 125.550, 79.830
Angle α, β, γ (deg.)90.00, 96.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA GYRASE SUBUNIT B /


Mass: 42721.449 Da / Num. of mol.: 2 / Fragment: 43K domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LCX5, UniProt: Q5SHZ4*PLUS, EC: 5.99.1.3
#2: Chemical ChemComp-NOV / NOVOBIOCIN / 4-Hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)benzamido]-8-methylcoumarin-7-yl 3-O-carbamoyl-5,5-di-C-methyl-alpha-l-lyxofuranoside / Novobiocin


Mass: 612.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H36N2O11 / Comment: antibiotic*YM
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris,sodium formate, sodium cacodylate, KCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14.5 mg/mlprotein1drop
210 mMTris1reservoirpH7.2
31 mMEDTA1reservoirpH8.0
45 mM2-mercaptoethanol1reservoir
5200 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9397 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 25, 2000
RadiationMonochromator: fast-scan double diamond monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9397 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. all: 37265 / Num. obs: 37265 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 5.5 / % possible all: 90.4
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 15 Å / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Rmerge(I) obs: 0.155

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→14.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1591871.55 / Data cutoff high rms absF: 1591871.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2765 7.5 %RANDOM
Rwork0.206 ---
obs0.206 37265 94.9 %-
all-37265 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.5215 Å2 / ksol: 0.368755 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.82 Å2
2---2.44 Å20 Å2
3---2.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-15 Å
Luzzati sigma a0.25 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.3→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5936 0 94 468 6498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 394 7.4 %
Rwork0.226 4953 -
obs-3478 83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NOVO1.XPRM
X-RAY DIFFRACTION4FORMAT.XPRM
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Rfactor Rfree: 0.302 / Rfactor Rwork: 0.226 / Rfactor obs: 0.226

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