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- PDB-3l6v: Crystal Structure of the Xanthomonas campestris Gyrase A C-termin... -

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Basic information

Entry
Database: PDB / ID: 3l6v
TitleCrystal Structure of the Xanthomonas campestris Gyrase A C-terminal Domain
ComponentsDNA gyrase subunit A
KeywordsISOMERASE / gyrase A C-terminal domain / GyrA C-terminal domain / DNA wrapping / beta-strand-bearing proline / ATP-binding / Nucleotide-binding / Topoisomerase
Function / homology
Function and homology information


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 / DNA-templated DNA replication / chromosome / 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 / 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/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 / 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 speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.19 Å
AuthorsHsieh, T.J. / Yen, T.J. / Lin, T.S. / Chang, H.T. / Huang, S.Y. / Farh, L. / Chan, N.L.
CitationJournal: To be Published
Title: Twisting of the DNA binding surface by a beta-strand-bearing proline modulates DNA gyrase activity
Authors: Hsieh, T.J. / Yen, T.J. / Lin, T.S. / Chang, H.T. / Huang, S.Y. / Farh, L. / Chan, N.L.
History
DepositionDec 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,8412
Polymers79,8412
Non-polymers00
Water3,171176
1
A: DNA gyrase subunit A


Theoretical massNumber of molelcules
Total (without water)39,9211
Polymers39,9211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit A


Theoretical massNumber of molelcules
Total (without water)39,9211
Polymers39,9211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.494, 58.968, 74.415
Angle α, β, γ (deg.)79.00, 79.78, 69.62
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA gyrase subunit A / / GyrA


Mass: 39920.664 Da / Num. of mol.: 2 / Fragment: C-terminal domain / Mutation: L530M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: gyrA, XCC1574 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PAB1, EC: 5.99.1.3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 200mM ammonium sulfate, 100mM Bis-Tris pH 5.2-5.9, 25-29% (v/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL12B210.97960, 0.96430
SYNCHROTRONNSRRC BL13B121
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDOct 16, 2006
ADSC QUANTUM 3152CCDNov 2, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromator (DCM)MADMx-ray1
2LN2-cooled, fixed-exit double crystal monochromator Si(1 1 1)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.96431
311
ReflectionResolution: 2.19→29 Å / Num. all: 41787 / Num. obs: 40325 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044
Reflection shellResolution: 2.19→2.25 Å / Rmerge(I) obs: 0.109 / % possible all: 92.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.19→29 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.889 / SU B: 5.305 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27059 2022 5 %RANDOM
Rwork0.2187 ---
all0.22123 41787 --
obs0.22123 38303 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.405 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0.23 Å20.37 Å2
2--1.11 Å20.63 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.19→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4745 0 0 176 4921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224808
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.9696494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8185613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.20522.153209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.97815847
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8521561
X-RAY DIFFRACTIONr_chiral_restr0.1570.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213581
X-RAY DIFFRACTIONr_mcbond_it1.0991.53042
X-RAY DIFFRACTIONr_mcangle_it2.0224886
X-RAY DIFFRACTIONr_scbond_it3.00831766
X-RAY DIFFRACTIONr_scangle_it4.954.51608
LS refinement shellResolution: 2.191→2.248 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 132 -
Rwork0.235 2718 -
obs--92.83 %

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