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- PDB-4uro: Crystal Structure of Staph GyraseB 24kDa in complex with Novobiocin -

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Basic information

Entry
Database: PDB / ID: 4uro
TitleCrystal Structure of Staph GyraseB 24kDa in complex with Novobiocin
ComponentsDNA GYRASE SUBUNIT B
KeywordsISOMERASE / ANTIBIOTICS / 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
NOVOBIOCIN / DNA gyrase subunit B
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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
DepositionJul 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 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)105,2058
Polymers102,7544
Non-polymers2,4504
Water1,22568
1
A: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3012
Polymers25,6891
Non-polymers6131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3012
Polymers25,6891
Non-polymers6131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3012
Polymers25,6891
Non-polymers6131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3012
Polymers25,6891
Non-polymers6131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.280, 68.590, 85.720
Angle α, β, γ (deg.)90.00, 91.72, 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-NOV / NOVOBIOCIN / 4-Hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)benzamido]-8-methylcoumarin-7-yl 3-O-carbamoyl-5,5-di-C-methyl-alpha-l-lyxofuranoside / Novobiocin


Mass: 612.624 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H36N2O11 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.12 Å3/Da / Density % sol: 42.09 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH8.5, 30% PEG 3350

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Type: ALS / Wavelength: 1
DetectorDate: Oct 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→74.24 Å / Num. obs: 26992 / % possible obs: 99.6 % / Observed criterion σ(I): 3.3 / Redundancy: 3.7 % / Biso Wilson estimate: 53.44 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.9
Reflection shellResolution: 2.59→2.89 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AJ6

1aj6


Resolution: 2.59→74.24 Å / Cor.coef. Fo:Fc: 0.9065 / Cor.coef. Fo:Fc free: 0.8635 / SU R Cruickshank DPI: 0.71 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.616 / SU Rfree Blow DPI: 0.29 / SU Rfree Cruickshank DPI: 0.301
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 1348 5 %RANDOM
Rwork0.1951 ---
obs0.1978 26939 99.54 %-
Displacement parametersBiso mean: 43.35 Å2
Baniso -1Baniso -2Baniso -3
1--6.3088 Å20 Å21.5912 Å2
2--12.0503 Å20 Å2
3----5.7415 Å2
Refine analyzeLuzzati coordinate error obs: 0.282 Å
Refinement stepCycle: LAST / Resolution: 2.59→74.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5733 0 176 68 5977
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016015HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.178204HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2066SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes177HARMONIC8
X-RAY DIFFRACTIONt_gen_planes977HARMONIC8
X-RAY DIFFRACTIONt_it6015HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.13
X-RAY DIFFRACTIONt_other_torsion24.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion811SEMIHARMONIC5
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_contact6777SEMIHARMONIC4
LS refinement shellResolution: 2.59→2.69 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2649 137 4.82 %
Rwork0.1994 2703 -
all0.2031 2840 -
obs--99.54 %

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