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

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Basic information

Entry
Database: PDB / ID: 4wud
TitleN-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from no salt 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 strain K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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 1.2Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9055
Polymers43,3161
Non-polymers5894
Water2,504139
1
A: DNA gyrase subunit B
hetero molecules

A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,80910
Polymers86,6322
Non-polymers1,1788
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7870 Å2
ΔGint-95 kcal/mol
Surface area30090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.800, 141.480, 80.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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 K-12 (bacteria)
Gene: gyrB, acrB, himB, hisU, nalC, parA, pcbA, b3699, JW5625
Plasmid: pAJ1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: P0AES6, EC: 5.99.1.3

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Non-polymers , 5 types, 143 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-NA / SODIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
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: I04-1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.95→27.54 Å / Num. obs: 36686 / % possible obs: 99.7 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.026 / Net I/σ(I): 15.9 / Num. measured all: 217252
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
1.95-260.8332.31599826710.650.37299.7
8.72-27.545.50.0284025324580.9990.01397.3

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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: 1.95→27.54 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2208 / WRfactor Rwork: 0.1874 / FOM work R set: 0.8283 / SU B: 7.184 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1369 / SU Rfree: 0.1302 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 1894 5.2 %RANDOM
Rwork0.1847 34791 --
obs0.1864 34791 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.99 Å2 / Biso mean: 43.195 Å2 / Biso min: 25.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2--2.53 Å20 Å2
3----1.22 Å2
Refinement stepCycle: final / Resolution: 1.95→27.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 34 140 3094
Biso mean--31.8 44.63 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193026
X-RAY DIFFRACTIONr_bond_other_d0.0010.022824
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9444110
X-RAY DIFFRACTIONr_angle_other_deg0.78736484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4035388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31924.38137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80615495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6961518
X-RAY DIFFRACTIONr_chiral_restr0.0770.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023529
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02687
X-RAY DIFFRACTIONr_mcbond_it1.4872.5761540
X-RAY DIFFRACTIONr_mcbond_other1.4882.5751539
X-RAY DIFFRACTIONr_mcangle_it2.1343.8551923
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 138 -
Rwork0.396 2512 -
all-2650 -
obs--99.55 %
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)
13.420.8327-0.09221.1520.13491.3568-0.1860.0183-0.45610.0460.0909-0.16850.13330.15650.09510.09640.0310.05720.02640.00240.104717.36622.1193-18.7036
20.73130.23690.45656.90851.06271.535-0.0310.07730.206-0.2930.02890.3535-0.21750.05350.0020.10870.0263-0.0390.02950.00270.118410.183148.2124-3.8136
38.0039-2.7315-8.13591.02192.80568.2806-0.21911.1047-0.42650.2177-0.33070.38180.3308-1.13140.54990.77610.06050.0210.3173-0.11080.82571.249161.4414-3.2643
40.301-0.31460.10353.285-0.22990.8954-0.0356-0.04690.04690.00960.01690.6988-0.0958-0.16470.01870.11560.0239-0.0560.0497-0.02780.25454.019850.3079-4.4751
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 218
2X-RAY DIFFRACTION2A219 - 299
3X-RAY DIFFRACTION3A300 - 318
4X-RAY DIFFRACTION4A319 - 392

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