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- PDB-4urm: Crystal Structure of Staph GyraseB 24kDa in complex with Kibdelomycin -

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Basic information

Entry
Database: PDB / ID: 4urm
TitleCrystal Structure of Staph GyraseB 24kDa in complex with Kibdelomycin
ComponentsDNA GYRASE SUBUNIT B
KeywordsISOMERASE / ANTIBIOTICS / GYRASE / TOPOISOMERASE IV / NATURAL PRODUCT
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / 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. ...DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / 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 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-XAM / DNA gyrase subunit B
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.94 Å
AuthorsLu, J. / Patel, S. / Sharma, N. / Soisson, S. / Kishii, R. / Takei, M. / Fukuda, Y. / Lumb, K.J. / Singh, S.B.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Structures of Kibdelomycin Bound to Staphylococcus Aureus Gyrb and Pare Showed a Novel U-Shaped Binding Mode.
Authors: Lu, J. / Patel, S. / Sharma, N. / Soisson, S.M. / Kishii, R. / Takei, M. / Fukuda, Y. / Lumb, K.J. / Singh, S.B.
History
DepositionJun 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA GYRASE SUBUNIT B
B: DNA GYRASE SUBUNIT B
C: DNA GYRASE SUBUNIT B
D: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5148
Polymers102,7544
Non-polymers3,7594
Water32418
1
A: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6282
Polymers25,6891
Non-polymers9401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6282
Polymers25,6891
Non-polymers9401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6282
Polymers25,6891
Non-polymers9401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6282
Polymers25,6891
Non-polymers9401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.280, 75.550, 90.450
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA GYRASE SUBUNIT B / / GYRASEB


Mass: 25688.619 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P0A0K8, EC: 5.99.1.3
#2: Chemical
ChemComp-XAM / (1R,4aS,5S,6S,8aR)-5-{[(5S)-1-(3-O-acetyl-4-O-carbamoyl-6-deoxy-2-O-methyl-alpha-L-talopyranosyl)-4-hydroxy-2-oxo-5-(propan-2-yl)-2,5-dihydro-1H-pyrrol-3-yl]carbonyl}-6-methyl-4-methylidene-1,2,3,4,4a,5,6,8a-octahydronaphthalen-1-yl 2,6-dideoxy-3-C-[(1S)-1-{[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)carbonyl]amino}ethyl]-beta-D-ribo-hexopyranoside / Amycolamicin


Mass: 939.872 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H60Cl2N4O14
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.3 Å3/Da / Density % sol: 46.61 % / Description: NONE
Crystal growpH: 8.5
Details: 0.12M MAGNESIUM CHLORIDE, 0.06 M TRIS PH8.5, 15% PEG 3350

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.93→90.45 Å / Num. obs: 20139 / % possible obs: 99.7 % / Observed criterion σ(I): 2.7 / Redundancy: 3.7 % / Biso Wilson estimate: 66.18 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 3.7
Reflection shellResolution: 2.93→90.45 Å

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Processing

SoftwareName: BUSTER / Version: 2.11.5 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.94→30.44 Å / Cor.coef. Fo:Fc: 0.9051 / Cor.coef. Fo:Fc free: 0.8493 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.401
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 1012 5.06 %RANDOM
Rwork0.1953 ---
obs0.1984 20004 99.71 %-
Displacement parametersBiso mean: 49.38 Å2
Baniso -1Baniso -2Baniso -3
1-5.2479 Å20 Å2-2.3384 Å2
2--8.1216 Å20 Å2
3----13.3695 Å2
Refine analyzeLuzzati coordinate error obs: 0.346 Å
Refinement stepCycle: LAST / Resolution: 2.94→30.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5875 0 256 18 6149
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016253HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.258558HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2195SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes166HARMONIC8
X-RAY DIFFRACTIONt_gen_planes979HARMONIC8
X-RAY DIFFRACTIONt_it6253HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.86
X-RAY DIFFRACTIONt_other_torsion20.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion873SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7255SEMIHARMONIC4
LS refinement shellResolution: 2.94→3.1 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2851 135 4.63 %
Rwork0.2162 2780 -
all0.2195 2915 -
obs--99.71 %

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