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- PDB-4elz: CCDBVFI:GYRA14VFI -

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Basic information

Entry
Database: PDB / ID: 4elz
TitleCCDBVFI:GYRA14VFI
Components
  • CcdB
  • 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 topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / 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 / 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
Cytotoxic protein CcdB / DNA gyrase subunit A
Similarity search - Component
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDe Jonge, N. / Simic, M. / 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: 3KUA
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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)58,3755
Polymers58,2834
Non-polymers921
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-35 kcal/mol
Surface area21490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.505, 94.590, 120.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA gyrase subunit A


Mass: 17261.693 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 362-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (bacteria) / Strain: ATCC 700601 / ES114 / Gene: gyrA, VF_1204 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5E5J7, EC: 5.99.1.3
#2: Protein CcdB


Mass: 11879.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (bacteria) / Strain: MJ11 / Gene: CcdB, VFMJ11_A0651 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): B462 / References: UniProt: B5EU32
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 1.2M NAH2PO4, 0.8M K2HPO4, 100MM CAPS, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2.131→16.94 Å / Num. all: 29888 / Num. obs: 32823 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 44.6 % / Biso Wilson estimate: 31.84 Å2 / Rmerge(I) obs: 0.156 / Rsym value: 0.156 / Net I/σ(I): 15

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KU8

3ku8
PDB Unreleased entry


Resolution: 2.2→16.939 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1537 5.06 %RANDOM
Rwork0.1947 ---
obs0.1974 30404 95.85 %-
all-30404 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.913 Å2 / ksol: 0.409 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6274 Å2-0 Å20 Å2
2---0.0037 Å2-0 Å2
3----1.6238 Å2
Refinement stepCycle: LAST / Resolution: 2.2→16.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3659 0 6 193 3858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083739
X-RAY DIFFRACTIONf_angle_d1.0825088
X-RAY DIFFRACTIONf_dihedral_angle_d13.8431358
X-RAY DIFFRACTIONf_chiral_restr0.075616
X-RAY DIFFRACTIONf_plane_restr0.005648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.27090.29051150.2462598X-RAY DIFFRACTION96
2.2709-2.35190.32021500.22312526X-RAY DIFFRACTION94
2.3519-2.44580.29431300.22892538X-RAY DIFFRACTION94
2.4458-2.55680.27191390.22242524X-RAY DIFFRACTION93
2.5568-2.69110.27551330.21662524X-RAY DIFFRACTION93
2.6911-2.85890.31111410.20822512X-RAY DIFFRACTION93
2.8589-3.07840.27091360.20042557X-RAY DIFFRACTION94
3.0784-3.3860.28821430.19662685X-RAY DIFFRACTION98
3.386-3.87090.21141510.18262738X-RAY DIFFRACTION100
3.8709-4.85770.191370.15332773X-RAY DIFFRACTION100
4.8577-16.93970.23691620.20272892X-RAY DIFFRACTION100
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)
13.0223-1.26131.3053.5177-1.30661.51240.0570.0402-0.17530.1344-0.0892-0.19080.01430.17830.01980.0806-0.02860.02420.1249-0.00520.091525.012-29.554-47.1118
22.2837-1.3994-0.88082.79280.99551.80060.11910.10350.3872-0.1266-0.110.1022-0.3165-0.1210.02970.1946-0.0175-0.02980.12380.00530.22095.6683-1.6922-48.4181
33.55230.8555-0.00655.0158-1.25953.1755-0.1541-0.0647-0.16210.06990.18270.08490.0391-0.348-0.01550.17-0.06740.01660.1472-0.00660.10716.4142-23.6106-26.8668
43.27970.1671-0.49784.5292-0.01242.8541-0.1424-0.19350.11560.34320.0441-0.45620.01830.16530.06340.176-0.0563-0.07510.209-0.00350.209420.6824-8.0463-26.2625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 352:494
2X-RAY DIFFRACTION2chain B and resi 362:492
3X-RAY DIFFRACTION3chain C and resi 2:105
4X-RAY DIFFRACTION4chain D and resi 2:105

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