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- PDB-4prv: E. coli GyrB 43-kDa N-terminal fragment in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 4prv
TitleE. coli GyrB 43-kDa N-terminal fragment in complex with ADP
ComponentsGyrBDNA gyrase
KeywordsISOMERASE / GyrB / ATP hydrolysis
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 / cytosol / cytoplasm
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
ADENOSINE-5'-DIPHOSPHATE / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsStanger, F.V. / Schirmer, T.
CitationJournal: Plos One / Year: 2014
Title: Structure of the N-Terminal Gyrase B Fragment in Complex with ADPPi Reveals Rigid-Body Motion Induced by ATP Hydrolysis
Authors: Stanger, F.V. / Dehio, C. / Schirmer, T.
History
DepositionMar 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: GyrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5703
Polymers44,1191
Non-polymers4522
Water2,270126
1
A: GyrB
hetero molecules

A: GyrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1406
Polymers88,2372
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6400 Å2
ΔGint-54 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.250, 142.520, 79.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-626-

HOH

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Components

#1: Protein GyrB / DNA gyrase


Mass: 44118.641 Da / Num. of mol.: 1 / Fragment: UNP residues 2-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pRSFDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AES6, EC: 5.99.1.3
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.05 Å3/Da / Density % sol: 59.3 % / Mosaicity: 0.198 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10%(w/v) PEG20000, 20%(v/v) PEGMME550, 0.02M each carboxylic acid, 0.1M bicine/Trizma base pH 8.5, vapor diffusion, sitting drop, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→75.03 Å / Num. all: 30053 / Num. obs: 30053 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.303 Å2 / Rmerge(I) obs: 0.068 / Χ2: 0.951 / Net I/σ(I): 22.15
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.120.9350.5833.3229579538051550.64495.8
2.12-2.270.9470.3655.2424254526737220.39670.7
2.27-2.450.9810.2159.0429817471743960.23293.2
2.45-2.680.990.15312.5424990433837150.16585.6
2.68-30.9960.08520.2322830404536730.09290.8
3-3.460.9990.04933.3921561353332420.05491.8
3.46-4.240.9990.0315015759303323940.03478.9
4.24-5.9810.02459.7714856237823750.02699.9
5.98-75.030.9990.01971.359082138213810.02199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å75.03 Å
Translation3.5 Å75.03 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EI1

1ei1


Resolution: 2→75.03 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.2265 / WRfactor Rwork: 0.1778 / FOM work R set: 0.7899 / SU B: 4.384 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1913 / SU Rfree: 0.1808 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 2011 6.7 %RANDOM
Rwork0.2067 ---
obs0.2102 30052 88.22 %-
all-30052 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.4 Å2 / Biso mean: 28.952 Å2 / Biso min: 13.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å2-0 Å20 Å2
2--1.97 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2→75.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 28 126 2982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192940
X-RAY DIFFRACTIONr_bond_other_d0.0010.022746
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.9583993
X-RAY DIFFRACTIONr_angle_other_deg0.91536306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.295373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.49624.526137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16515481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3231517
X-RAY DIFFRACTIONr_chiral_restr0.120.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023385
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02673
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 164 -
Rwork0.287 2261 -
all-2425 -
obs--97.39 %

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