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- PDB-4urn: Crystal Structure of Staph ParE 24kDa in complex with Novobiocin -

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Entry
Database: PDB / ID: 4urn
TitleCrystal Structure of Staph ParE 24kDa in complex with Novobiocin
ComponentsDNA TOPOISOMERASE IV, B SUBUNITTopoisomerase
KeywordsISOMERASE / ANTIBIOTICS / GYRASE / NATURAL PRODUCT
Function / homologyHistidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 2-Layer Sandwich / Alpha Beta / NOVOBIOCIN / :
Function and homology information
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 16, 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:
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Assembly

Deposited unit
A: DNA TOPOISOMERASE IV, B SUBUNIT
B: DNA TOPOISOMERASE IV, B SUBUNIT
C: DNA TOPOISOMERASE IV, B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2286
Polymers74,3903
Non-polymers1,8383
Water90150
1
A: DNA TOPOISOMERASE IV, B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4092
Polymers24,7971
Non-polymers6131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA TOPOISOMERASE IV, B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4092
Polymers24,7971
Non-polymers6131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA TOPOISOMERASE IV, B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4092
Polymers24,7971
Non-polymers6131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.678, 75.321, 76.144
Angle α, β, γ (deg.)90.00, 92.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA TOPOISOMERASE IV, B SUBUNIT / Topoisomerase / PARE


Mass: 24796.766 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: X5EN43, EC: 5.99.1.-
#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.: 3 / Source method: obtained synthetically / Formula: C31H36N2O11 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.23 Å3/Da / Density % sol: 44.76 % / Description: NONE
Crystal growpH: 7.5
Details: 0.15M AMMONIUM ACETATE, 0.075M TRIS PH 8.5 AND 19% PEG 3350

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 28285 / % possible obs: 97 % / Observed criterion σ(I): 3.46 / Redundancy: 4.1 % / Biso Wilson estimate: 48.81 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.3
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.46 / % possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S14

1s14


Resolution: 2.3→19.47 Å / Cor.coef. Fo:Fc: 0.8844 / Cor.coef. Fo:Fc free: 0.8583 / SU R Cruickshank DPI: 0.333 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.311 / SU Rfree Blow DPI: 0.236 / SU Rfree Cruickshank DPI: 0.245
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 1416 5.03 %RANDOM
Rwork0.2225 ---
obs0.2248 28173 96.76 %-
Displacement parametersBiso mean: 50.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.9806 Å20 Å2-5.1514 Å2
2--19.3465 Å20 Å2
3----17.3659 Å2
Refine analyzeLuzzati coordinate error obs: 0.338 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4199 0 132 50 4381
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014429HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.236002HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1552SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes111HARMONIC8
X-RAY DIFFRACTIONt_gen_planes726HARMONIC8
X-RAY DIFFRACTIONt_it4429HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.06
X-RAY DIFFRACTIONt_other_torsion18.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion577SEMIHARMONIC5
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_contact4869SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.39 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2853 160 5.41 %
Rwork0.2397 2797 -
all0.2423 2957 -
obs--96.76 %

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