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- PDB-1suu: Structure of DNA gyrase A C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 1suu
TitleStructure of DNA gyrase A C-terminal domain
ComponentsDNA gyrase subunit A
KeywordsISOMERASE / topoisomerase / DNA gyrase / beta-propeller / beta-pinwheel
Function / homology
Function and homology information


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
DNA gyrase/topoisomerase IV, subunit A, C-terminal / 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, C-terminal / 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 / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
DNA gyrase subunit A
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsCorbett, K.D. / Shultzaberger, R.K. / Berger, J.M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold.
Authors: Corbett, K.D. / Shultzaberger, R.K. / Berger, J.M.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA gyrase subunit A


Theoretical massNumber of molelcules
Total (without water)34,5091
Polymers34,5091
Non-polymers00
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.523, 82.294, 88.470
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: 34508.723 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: GYRA, BB0435 / Production host: Escherichia coli (E. coli) / References: UniProt: O51396, EC: 5.99.1.3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: sodium phosphate, PEG-3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.127, 0.9796, 1.0199
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 3, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Double crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.1271
20.97961
31.01991
ReflectionResolution: 1.75→30 Å / Num. all: 31419 / Num. obs: 29828 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.037 / Net I/σ(I): 29.6
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 4.6 / Rsym value: 0.229 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
Blu-Icedata collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.401 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.123 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22505 1589 5.1 %RANDOM
Rwork0.19351 ---
all0.19508 29828 --
obs0.19508 29828 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.432 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å20 Å20 Å2
2---1.37 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 0 241 2491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222270
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.9823045
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5335290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021616
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2992
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2201
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7681.51440
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49922308
X-RAY DIFFRACTIONr_scbond_it2.5153830
X-RAY DIFFRACTIONr_scangle_it4.2894.5737
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 113 -
Rwork0.234 1960 -
obs-2073 91 %
Refinement TLS params.Method: refined / Origin x: 2.2897 Å / Origin y: 39.7972 Å / Origin z: 55.5032 Å
111213212223313233
T0.0086 Å20.0202 Å20.0138 Å2-0.0887 Å20.0036 Å2--0.0935 Å2
L0.2502 °20.2744 °20.0588 °2-1.5486 °20.1849 °2--1.5316 °2
S-0.0008 Å °0.0086 Å °-0.0086 Å °0.0723 Å °-0.0129 Å °-0.006 Å °0.0299 Å °0.017 Å °0.0137 Å °

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