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- PDB-4url: Crystal Structure of Staph ParE43kDa in complex with KBD -

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Basic information

Entry
Database: PDB / ID: 4url
TitleCrystal Structure of Staph ParE43kDa in complex with KBD
ComponentsDNA TOPOISOMERASE IV, B SUBUNIT
KeywordsISOMERASE / ANTIBIOTICS / NATURAL PRODUCT / KIBDELOMYCIN / GYRASE / TOPOISOMERASE IV
Function / homologyRibosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 2-Layer Sandwich / Alpha Beta / Chem-XAM / :
Function and homology information
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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 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:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,8544
Polymers89,9752
Non-polymers1,8802
Water1,910106
1
A: DNA TOPOISOMERASE IV, B SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9272
Polymers44,9871
Non-polymers9401
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)45,9272
Polymers44,9871
Non-polymers9401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.449, 136.809, 69.191
Angle α, β, γ (deg.)90.00, 111.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 44987.363 Da / Num. of mol.: 2 / Fragment: 43KDA N-TERMINAL DOMAIN, RESIDUES 1-406
Source method: isolated from a genetically manipulated source
Details: KIBDELOMYCIN / Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: X5EN43, Isomerases; Other isomerases; Sole sub-subclass for isomerases that do not belong in the other subclasses
#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.: 2 / Source method: obtained synthetically / Formula: C44H60Cl2N4O14
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.66 Å3/Da / Density % sol: 53.71 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2M AMMONIUM SULFATE, 0.1M TRIS PH 8.5 AND 25% 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: Feb 18, 2009
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: 41758 / % possible obs: 99.9 % / Observed criterion σ(I): 2.7 / Redundancy: 4 % / Biso Wilson estimate: 52.27 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 20.3 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S16

1s16


Resolution: 2.29→49.73 Å / Cor.coef. Fo:Fc: 0.9244 / Cor.coef. Fo:Fc free: 0.9004 / SU R Cruickshank DPI: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.26 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.215
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1311 3.14 %RANDOM
Rwork0.2168 ---
obs0.2179 41708 98.81 %-
Displacement parametersBiso mean: 53.93 Å2
Baniso -1Baniso -2Baniso -3
1--5.5474 Å20 Å2-13.5869 Å2
2--3.1737 Å20 Å2
3---2.3737 Å2
Refine analyzeLuzzati coordinate error obs: 0.348 Å
Refinement stepCycle: LAST / Resolution: 2.29→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5507 0 128 106 5741
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015736HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.217774HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2039SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes150HARMONIC8
X-RAY DIFFRACTIONt_gen_planes878HARMONIC8
X-RAY DIFFRACTIONt_it5736HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.18
X-RAY DIFFRACTIONt_other_torsion19.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion769SEMIHARMONIC5
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_contact6543SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2532 80 3 %
Rwork0.2482 2586 -
all0.2484 2666 -
obs--98.81 %

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