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

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Basic information

Entry
Database: PDB / ID: 4xtj
TitleN-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM KCl plus 100 mM NaCl 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 / Resolution: 1.92 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
DepositionJan 23, 2015Deposition 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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)43,7876
Polymers43,1591
Non-polymers6285
Water3,963220
1
A: DNA gyrase subunit B
hetero molecules

A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,57312
Polymers86,3172
Non-polymers1,25610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area8340 Å2
ΔGint-97 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.520, 140.910, 79.840
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: 43158.566 Da / Num. of mol.: 1
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, 225 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.: 220 / 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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15-25% (v/v) PEG 3350, 2 mM MgCl2, 100 mM KCl, 100 mM NaCl, 100 mM Tris-HCl pH 8.0
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→35.23 Å / Num. obs: 37803 / % possible obs: 99.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 27.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.029 / Net I/σ(I): 18.5 / Num. measured all: 199461
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
1.92-1.975.30.9151.91403326680.6990.43496.2
8.59-35.234.60.0258.920724490.9990.0193.8

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EI1

1ei1


Resolution: 1.92→35.23 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2017 / WRfactor Rwork: 0.1694 / FOM work R set: 0.8278 / SU B: 6.944 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1342 / SU Rfree: 0.1277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 1947 5.2 %RANDOM
Rwork0.1837 35855 --
obs0.1854 35855 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.12 Å2 / Biso mean: 36.3 Å2 / Biso min: 20.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--1.51 Å20 Å2
3----2.12 Å2
Refinement stepCycle: final / Resolution: 1.92→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 0 35 225 3179
Biso mean--28.36 40.04 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193034
X-RAY DIFFRACTIONr_bond_other_d0.0010.022834
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9434122
X-RAY DIFFRACTIONr_angle_other_deg0.77436506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2365390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54224.275138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52215497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1791519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023541
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02692
X-RAY DIFFRACTIONr_mcbond_it1.0822.2051542
X-RAY DIFFRACTIONr_mcbond_other1.0832.2051541
X-RAY DIFFRACTIONr_mcangle_it1.6143.3011926
LS refinement shellResolution: 1.921→1.971 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 124 -
Rwork0.3 2536 -
all-2660 -
obs--96.38 %
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)
13.18620.7128-0.24451.1478-0.12451.2423-0.2925-0.0552-0.40080.08180.0984-0.20090.14850.19030.19410.07380.04270.04750.04420.01870.092817.34922.0278-18.6016
21.17350.46390.39815.2911.35770.697-0.01610.15520.1744-0.3461-0.03870.2053-0.19220.04960.05490.07840.0253-0.01060.0944-0.00630.04569.86848.1366-3.9683
33.9941-1.9668-5.91121.80433.57519.28260.00320.61320.080.1183-0.32840.55910.1159-0.93250.32520.39190.0415-0.06130.2380.02220.50191.153361.2168-3.2745
40.11080.23550.00772.26840.27570.7141-0.0253-0.00120.09080.1023-0.04790.3945-0.0837-0.06780.07310.04720.0355-0.02450.1049-0.03430.13073.958350.0981-4.5785
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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