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- PDB-3tvr: Crystal Structure of Streptomyces coelicolor Polyketide Aromatase... -

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Basic information

Entry
Database: PDB / ID: 3tvr
TitleCrystal Structure of Streptomyces coelicolor Polyketide Aromatase/Cyclase whiE-ORFVI
ComponentsPolyketide cyclase
KeywordsUNKNOWN FUNCTION / Helix-grip fold / polyketide aromatase/cyclase / polyketide binding
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 / 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. / 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
DepositionSep 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Jun 20, 2018Group: Data collection / Category: diffrn_radiation
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_scattering_type
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8412
Polymers19,7491
Non-polymers921
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.702, 42.060, 47.999
Angle α, β, γ (deg.)90.00, 91.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyketide cyclase / WhiE ORF VI


Mass: 19749.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SC6G9.18, SCO5315, whiE ORFVI / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23154
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 0.1M Bis-Tris, 0.2M magnesium chloride, 28% PEG 3350, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-3 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 5, 2007
RadiationMonochromator: Si (220) phi=0, Si(220) phi=90, double-crystal, nonfixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 17903 / % possible obs: 99.7 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.86 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2RER

2rer


Resolution: 1.8→34.39 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.689 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21414 1792 10.1 %RANDOM
Rwork0.17049 ---
obs0.17503 15892 98.75 %-
all-17903 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.056 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å2-1.39 Å2
2---0.71 Å2-0 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 6 199 1579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191411
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.9151919
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6815170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07223.42573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20115224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8471514
X-RAY DIFFRACTIONr_chiral_restr0.1680.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211100
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 109 -
Rwork0.2 1015 -
obs--88.02 %

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