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- PDB-3tl1: Crystal structure of the Streptomyces coelicolor WhiE ORFVI polyk... -

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Basic information

Entry
Database: PDB / ID: 3tl1
TitleCrystal structure of the Streptomyces coelicolor WhiE ORFVI polyketide aromatase/cyclase
ComponentsPolyketide cyclase
KeywordsBIOSYNTHETIC PROTEIN / Helix-grip fold / polyketide C9-C14 aromatase/cyclase / linear poly-beta-ketone intermediate
Function / homologyCoenzyme Q-binding protein COQ10, START domain / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Chem-JRO / Putative polyketide cyclase
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLee, M.-Y. / Ames, B.D. / Zhang, W. / Tang, Y. / Tsai, S.-C.
CitationJournal: Biochemistry / Year: 2012
Title: Insight into the Molecular Basis of Aromatic Polyketide Cyclization: Crystal Structure and in Vitro Characterization of WhiE-ORFVI.
Authors: Lee, M.Y. / Ames, B.D. / Tsai, S.C.
History
DepositionAug 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Polyketide cyclase
B: Polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2257
Polymers36,4332
Non-polymers7935
Water2,990166
1
A: Polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6594
Polymers18,2161
Non-polymers4423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polyketide cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5673
Polymers18,2161
Non-polymers3502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.517, 40.488, 66.806
Angle α, β, γ (deg.)90.00, 102.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyketide cyclase / WhiE ORF VI


Mass: 18216.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO5315, SC6G9.18 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23154
#2: Chemical ChemComp-JRO / 6,7,9-trihydroxy-3-methyl-1H-benzo[g]isochromen-1-one


Mass: 258.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M Bis-Tris pH5.4, 0.2M magnesium chloride, 30% PEG3350, 5mM JRSi284 (ligand), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2009
RadiationMonochromator: Double crystal, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→65.37 Å / Num. obs: 31201 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.8→1.86 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→41.29 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.028 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25387 3127 10 %RANDOM
Rwork0.18262 ---
obs0.1898 28074 98.8 %-
all-31201 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20.37 Å2
2---0.25 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 56 166 2758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222651
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.9413611
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20223.731134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80315426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8341526
X-RAY DIFFRACTIONr_chiral_restr0.1110.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022052
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21142
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21796
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2156
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6571.51623
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44922558
X-RAY DIFFRACTIONr_scbond_it3.62931367
X-RAY DIFFRACTIONr_scangle_it5.5724.51053
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 202 -
Rwork0.196 1891 -
obs--90.45 %

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