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- PDB-4yzr: Bacillus subtilis 168 Bacillaene Polyketide Synthase (PKS) Cytoch... -

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Basic information

Entry
Database: PDB / ID: 4yzr
TitleBacillus subtilis 168 Bacillaene Polyketide Synthase (PKS) Cytochrome P450 PksS
ComponentsPolyketide biosynthesis cytochrome P450 PksS
KeywordsOXIDOREDUCTASE / cytochrome P450 / Bacillaene biosynthesis / Polyketide Synthase
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / antibiotic biosynthetic process / monooxygenase activity / iron ion binding / heme binding / plasma membrane
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HISTIDINE / Polyketide biosynthesis cytochrome P450 PksS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRace, P.R. / Zulkepli, A.Z. / Anderson, R.J.L.
CitationJournal: To Be Published
Title: Bacillus subtilis 168 Bacillaene Polyketide Synthase (PKS) Cytochrome P450 PksS
Authors: Race, P.R. / Zulkepli, A.Z. / Anderson, R.J.L.
History
DepositionMar 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide biosynthesis cytochrome P450 PksS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5713
Polymers46,7981
Non-polymers7732
Water5,549308
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-24 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.810, 66.690, 74.540
Angle α, β, γ (deg.)90.00, 107.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyketide biosynthesis cytochrome P450 PksS


Mass: 46797.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: pksS, BSU17230 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O31785, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10N3O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus TM screen Condition B1: 0.09 M Halogen, 0.1 M Imidazole, MES pH 6.5, 30% P550MME-P20K
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→46.65 Å / Num. obs: 98866 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
Cootmodel building
SCALAdata scaling
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A50

3a50


Resolution: 1.35→46.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.937 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21087 4920 5 %RANDOM
Rwork0.18253 ---
obs0.18395 93691 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.476 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.35→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 43 308 3493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0193282
X-RAY DIFFRACTIONr_bond_other_d0.0030.023165
X-RAY DIFFRACTIONr_angle_refined_deg2.3931.9774444
X-RAY DIFFRACTIONr_angle_other_deg1.17937284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5025393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1923.885157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22115593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.671524
X-RAY DIFFRACTIONr_chiral_restr0.1620.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213669
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02774
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0141.6571560
X-RAY DIFFRACTIONr_mcbond_other2.0091.6561559
X-RAY DIFFRACTIONr_mcangle_it2.8062.4771948
X-RAY DIFFRACTIONr_mcangle_other2.8062.4781949
X-RAY DIFFRACTIONr_scbond_it3.6062.0351722
X-RAY DIFFRACTIONr_scbond_other3.6082.0361720
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1892.8972493
X-RAY DIFFRACTIONr_long_range_B_refined6.31314.1514030
X-RAY DIFFRACTIONr_long_range_B_other6.23813.7153874
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.355→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 335 -
Rwork0.282 6816 -
obs--98.49 %

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