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- PDB-7d78: The structure of thioesterase DcsB -

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Basic information

Entry
Database: PDB / ID: 7d78
TitleThe structure of thioesterase DcsB
ComponentsDltD domain-containing protein
KeywordsHYDROLASE / Thioesterase / Polyketides / Lactones
Function / homologySerine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / DltD domain-containing protein
Function and homology information
Biological speciesBeauveria bassiana
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96543121965 Å
AuthorsTang, Y. / Zhou, J.H. / Wang, G.Q.
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: A Polyketide Cyclase That Forms Medium-Ring Lactones.
Authors: Gao, D.W. / Jamieson, C.S. / Wang, G. / Yan, Y. / Zhou, J. / Houk, K.N. / Tang, Y.
History
DepositionOct 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DltD domain-containing protein
A: DltD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7799
Polymers70,3472
Non-polymers4327
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-31 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.707, 47.569, 71.695
Angle α, β, γ (deg.)90.000, 93.187, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11D-404-

CL

21D-552-

HOH

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Components

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Protein , 1 types, 2 molecules DA

#1: Protein DltD domain-containing protein / Thioesterase


Mass: 35173.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beauveria bassiana (strain ARSEF 2860) (fungus)
Strain: ARSEF 2860 / Gene: BBA_03809 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: J4WAT9

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Non-polymers , 5 types, 531 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 289.2 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M MIB, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 43010 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 24.1823539803 Å2 / CC1/2: 0.956 / Net I/σ(I): 26.44
Reflection shellResolution: 1.97→2 Å / Num. unique obs: 43010 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.96543121965→38.8402800782 Å / SU ML: 0.172334814659 / Cross valid method: FREE R-VALUE / σ(F): 1.36305408576 / Phase error: 17.7464889383
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.183022100251 2159 5.02607319117 %
Rwork0.145829863781 40797 -
obs0.147737692284 42956 99.3317146491 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.0832504375 Å2
Refinement stepCycle: LAST / Resolution: 1.96543121965→38.8402800782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4551 0 25 524 5100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006779309418354702
X-RAY DIFFRACTIONf_angle_d0.8120260151646360
X-RAY DIFFRACTIONf_chiral_restr0.0561821993983701
X-RAY DIFFRACTIONf_plane_restr0.00561864012093832
X-RAY DIFFRACTIONf_dihedral_angle_d4.804637411123972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.01110.2420576670271380.1657076828962571X-RAY DIFFRACTION95.656779661
2.0111-2.06140.1862982967691380.1565554159132708X-RAY DIFFRACTION99.0947075209
2.0614-2.11720.2162256724251540.1475034988592662X-RAY DIFFRACTION99.4350282486
2.1172-2.17950.1879786322421260.1493385112352741X-RAY DIFFRACTION99.5831886072
2.1795-2.24980.2135212840431630.1481855915982707X-RAY DIFFRACTION99.4800693241
2.2498-2.33020.1981990143981240.1501224750082708X-RAY DIFFRACTION99.5430579965
2.3302-2.42350.2224003467691610.1530953239762695X-RAY DIFFRACTION99.8601398601
2.4235-2.53380.1898663634351470.1566958836032724X-RAY DIFFRACTION99.9651810585
2.5338-2.66730.2302411380671200.1592287948892748X-RAY DIFFRACTION99.8955067921
2.6673-2.83440.1825134442521260.1572924422682717X-RAY DIFFRACTION99.7543859649
2.8344-3.05320.1945399824771570.161620606812744X-RAY DIFFRACTION99.9311057527
3.0532-3.36030.1984648727671500.1532660512482738X-RAY DIFFRACTION99.792674499
3.3603-3.84610.1715991031091460.1388093449052754X-RAY DIFFRACTION99.7592019264
3.8461-4.84420.1350447942241410.1233550818232781X-RAY DIFFRACTION99.8632946001
4.8442-4.84420.1677306548111680.1357964136282799X-RAY DIFFRACTION98.4732824427

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