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- PDB-4ely: CCDBVFI:GYRA14EC -

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Basic information

Entry
Database: PDB / ID: 4ely
TitleCCDBVFI:GYRA14EC
Components
  • CcdBChristian Commission for Development in Bangladesh
  • DNA gyrase subunit A
KeywordsTOXIN/ISOMERASE / ALPHA+BETA / TOPOISOMERASE / TOXIN-ISOMERASE complex
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / plasmid maintenance / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Toxin CcdB / CcdB protein / Topoisomerase, domain 3 / Topoisomerase; domain 3 / SH3 type barrels. - #110 / Plasmid maintenance toxin/Cell growth inhibitor / 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 ...Toxin CcdB / CcdB protein / Topoisomerase, domain 3 / Topoisomerase; domain 3 / SH3 type barrels. - #110 / Plasmid maintenance toxin/Cell growth inhibitor / 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 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 topoisomerase, type IIA-like domain superfamily / SH3 type barrels. / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA gyrase subunit A / Toxin CcdB
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Aliivibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.932 Å
AuthorsDe Jonge, N. / Simic, R. / Buts, L. / Haesaerts, S. / Roelants, K. / Garcia-Pino, A. / Sterckx, Y. / De Greve, H. / Lah, J. / Loris, R.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: Alternative interactions define gyrase specificity in the CcdB family.
Authors: De Jonge, N. / Simic, M. / Buts, L. / Haesaerts, S. / Roelants, K. / Garcia-Pino, A. / Sterckx, Y. / De Greve, H. / Lah, J. / Loris, R.
History
DepositionApr 11, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionMay 30, 2012ID: 3KU8
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit A
B: DNA gyrase subunit A
C: CcdB
D: CcdB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0607
Polymers58,8934
Non-polymers1673
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-51 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.073, 90.833, 58.130
Angle α, β, γ (deg.)90.00, 102.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-669-

HOH

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Components

#1: Protein DNA gyrase subunit A / / GYRA14


Mass: 17567.025 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 363-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: K12 / Gene: gyrA, GYRASE, S2444, SF2311 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AES5, EC: 5.99.1.3
#2: Protein CcdB / Christian Commission for Development in Bangladesh


Mass: 11879.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aliivibrio fischeri (bacteria) / Gene: ccdB / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): B462 / References: UniProt: Q84B82
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 56.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50MM MES, 1.6M (NH4)2SO4, 50MM MGCL2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.93→74 Å / Num. obs: 48855 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.99 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 19
Reflection shellResolution: 1.93→2.02 Å / Redundancy: 8.99 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 9.12 / Rsym value: 0.247 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3JSC AND 1X75

3jsc

1x75


Resolution: 1.932→24.624 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 2469 5.05 %random
Rwork0.1855 ---
obs0.1871 48849 98.91 %-
all-48849 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.558 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5609 Å20 Å2-2.8623 Å2
2---5.5203 Å2-0 Å2
3---4.9594 Å2
Refinement stepCycle: LAST / Resolution: 1.932→24.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3605 0 7 256 3868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083715
X-RAY DIFFRACTIONf_angle_d1.0665073
X-RAY DIFFRACTIONf_dihedral_angle_d15.0831372
X-RAY DIFFRACTIONf_chiral_restr0.07611
X-RAY DIFFRACTIONf_plane_restr0.005657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9322-1.96930.25781050.21292100X-RAY DIFFRACTION82
1.9693-2.00950.23751370.1992605X-RAY DIFFRACTION100
2.0095-2.05320.2221370.19092584X-RAY DIFFRACTION100
2.0532-2.10090.25661320.18572590X-RAY DIFFRACTION100
2.1009-2.15340.19451640.17482599X-RAY DIFFRACTION100
2.1534-2.21160.19321290.16982605X-RAY DIFFRACTION100
2.2116-2.27670.22831490.17482563X-RAY DIFFRACTION100
2.2767-2.35010.22961500.18462597X-RAY DIFFRACTION100
2.3501-2.4340.24051290.18912604X-RAY DIFFRACTION100
2.434-2.53140.23431380.19772599X-RAY DIFFRACTION100
2.5314-2.64640.22231430.19992629X-RAY DIFFRACTION100
2.6464-2.78580.25191270.19962594X-RAY DIFFRACTION100
2.7858-2.96010.24821290.20522600X-RAY DIFFRACTION100
2.9601-3.18820.2781330.20612632X-RAY DIFFRACTION100
3.1882-3.50820.2371550.19772580X-RAY DIFFRACTION100
3.5082-4.01390.18731400.18072628X-RAY DIFFRACTION100
4.0139-5.050.18241520.14912604X-RAY DIFFRACTION100
5.05-24.62550.20241200.19432667X-RAY DIFFRACTION99
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)
11.89650.01570.17193.65940.58861.6590.10460.2555-0.1067-0.4394-0.1773-0.15010.19680.1590.04210.22410.0713-0.00070.10920.00120.17998.458232.379826.5155
21.4117-0.2198-0.28252.37890.54551.97810.0451-0.35610.21580.475-0.14150.0339-0.127-0.07290.00910.1322-0.0793-0.02590.0847-0.09920.1052.249755.865650.7363
32.86880.8497-0.29443.81730.00042.62430.1029-0.10110.11140.004-0.1565-0.3347-0.30120.48630.04880.2618-0.0957-0.03470.32480.13060.312127.194853.437538.2938
42.3553-0.8421-0.03913.7401-0.43872.67430.008-0.4434-0.29710.351-0.037-0.10970.36790.36970.03710.3267-0.0117-0.06670.3670.18620.356125.243635.28548.5807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 363:497
2X-RAY DIFFRACTION2chain B and resseq 363:497
3X-RAY DIFFRACTION3chain C and resseq 2:105
4X-RAY DIFFRACTION4chain D and resseq 2:105

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