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- PDB-3nuh: A domain insertion in E. coli GyrB adopts a novel fold that plays... -

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Basic information

Entry
Database: PDB / ID: 3nuh
TitleA domain insertion in E. coli GyrB adopts a novel fold that plays a critical role in gyrase function
Components
  • DNA gyrase subunit A
  • DNA gyrase subunit B
KeywordsISOMERASE / gyrase / topoisomerase / supercoiling / specialization
Function / homology
Function and homology information


negative regulation of DNA-templated DNA replication / 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 ...negative regulation of DNA-templated DNA replication / 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 / identical protein binding / membrane / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Ubiquitin-like (UB roll) - #690 / GMP Synthetase; Chain A, domain 3 - #370 / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / Gyrase A; domain 2 - #40 / : / GyrB, hook / DNA gyrase subunit B insert domain ...Ubiquitin-like (UB roll) - #690 / GMP Synthetase; Chain A, domain 3 - #370 / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / Gyrase A; domain 2 - #40 / : / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / 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 / Toprim domain profile. / TOPRIM domain / GMP Synthetase; Chain A, domain 3 / Gyrase A; domain 2 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ubiquitin-like (UB roll) / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA gyrase subunit A / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 3.103 Å
AuthorsSchoeffler, A.J. / May, A.P. / Berger, J.M.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function.
Authors: Schoeffler, A.J. / May, A.P. / Berger, J.M.
History
DepositionJul 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit A
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9344
Polymers107,8862
Non-polymers492
Water1629
1
A: DNA gyrase subunit A
B: DNA gyrase subunit B
hetero molecules

A: DNA gyrase subunit A
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,8688
Polymers215,7714
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area11290 Å2
ΔGint-59 kcal/mol
Surface area79050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.062, 147.493, 138.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DNA gyrase subunit A / hisW / nalA / parD


Mass: 59658.840 Da / Num. of mol.: 1 / Fragment: unp residues 1-525
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: gyrA / Plasmid: pLIC172 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P0AES4, EC: 5.99.1.3
#2: Protein DNA gyrase subunit B / acrB / himB / hisU / nalC / parA / pcbA


Mass: 48226.742 Da / Num. of mol.: 1 / Fragment: unp residues 389-804
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: gyrB / Plasmid: pLIC172 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P0AES6, EC: 5.99.1.3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 8
Details: 90 mM imidazole pH 8.0, 11% isopropanol, 18 mM magnesium chloride, 10 mM spermidine, 3% pentaerythritol ethoxylate 15/4, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC Q315r / Detector: CCD / Date: Jul 22, 2008
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→35.6 Å / Num. obs: 20320 / % possible obs: 99.6 % / Redundancy: 5 % / Biso Wilson estimate: 56.37 Å2 / Rsym value: 0.103
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.387 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: molecular replacement-SAD
Starting model: The structure was solved as a combination of MR and SAD method. The starting model used corresponds to PDB ID 1AB4.

1ab4


Resolution: 3.103→35.6 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.763 / SU ML: 0.38 / σ(F): 1.9 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 3778 9.82 %
Rwork0.234 --
obs0.238 -99.26 %
all-38496 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.057 Å2 / ksol: 0.267 e/Å3
Displacement parametersBiso max: 232.93 Å2 / Biso mean: 82.602 Å2 / Biso min: 16.79 Å2
Baniso -1Baniso -2Baniso -3
1-41.129 Å2-0 Å2-0 Å2
2---21.17 Å20 Å2
3----19.959 Å2
Refinement stepCycle: LAST / Resolution: 3.103→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6666 0 2 9 6677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036770
X-RAY DIFFRACTIONf_angle_d0.6189141
X-RAY DIFFRACTIONf_chiral_restr0.0421033
X-RAY DIFFRACTIONf_plane_restr0.0021190
X-RAY DIFFRACTIONf_dihedral_angle_d12.642554
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.103-3.1430.3811250.3261146127187
3.143-3.1840.3741380.3031242138096
3.184-3.2270.3491350.2971236137199
3.227-3.2740.3511440.2761323146799
3.274-3.3220.2671380.26413031441100
3.322-3.3740.3691420.26413021444100
3.374-3.430.3331380.28112561394100
3.43-3.4890.3421440.27813101454100
3.489-3.5520.2971410.27812881429100
3.552-3.620.3231400.2713051445100
3.62-3.6940.2841350.25212811416100
3.694-3.7740.331380.23413111449100
3.774-3.8620.2691440.22612941438100
3.862-3.9580.2511430.20913131456100
3.958-4.0650.251380.21812571395100
4.065-4.1850.2631440.20413151459100
4.185-4.320.2521410.212861427100
4.32-4.4740.2591390.18412801419100
4.474-4.6530.2151420.17613051447100
4.653-4.8640.1911390.18312891428100
4.864-5.120.2731420.19713111453100
5.12-5.4390.2481400.21212771417100
5.439-5.8580.2921400.2212811421100
5.858-6.4440.2611410.2513131454100
6.444-7.3690.3161410.23712891430100
7.369-9.2570.2281440.20913161460100
9.257-35.6410.2311420.2071278142099
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)
10.3150.14010.23921.14780.08972.6117-0.0128-0.0979-0.0701-0.0464-0.10920.02040.8269-0.136500.3253-0.09860.07010.28360.00050.26966.4187-14.4691-9.0233
21.5553-0.0758-0.68140.77540.07021.33150.08560.0063-0.0929-0.2548-0.3463-0.13470.80780.10390.00260.52430.23230.10290.18950.02970.308524.0916-22.918-25.535
31.1538-0.6469-0.26830.6274-0.24051.26120.02270.1719-0.1564-0.20220.13180.04850.2563-0.520200.3589-0.3877-0.02440.56930.01950.2766-24.85-19.4442-6.0201
40.6732-0.0988-0.22381.6102-1.00461.5483-0.0448-0.01570.0728-0.1635-0.382-0.27780.16740.2983-00.16050.0547-0.00260.38610.13820.321525.8561-12.214824.6278
50.81291.24050.14282.1973-0.230.75870.1225-0.0288-0.05840.1995-0.1242-0.15680.3594-0.2164-00.3735-0.1450.00280.3605-0.04450.331-9.8848-37.607818.2237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain A and resseq 19:198A19 - 198
2X-RAY DIFFRACTION2Chain A and resseq 199:355A199 - 355
3X-RAY DIFFRACTION3Chain A and resseq 356:524A356 - 524
4X-RAY DIFFRACTION4Chain B and (resseq 403:533 or resseq 740:784)B403 - 533
5X-RAY DIFFRACTION4Chain B and (resseq 403:533 or resseq 740:784)B740 - 784
6X-RAY DIFFRACTION5Chain B and resseq 534:739B534 - 739

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