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- PDB-7d79: The structure of DcsB complex with its substrate analogue -

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Basic information

Entry
Database: PDB / ID: 7d79
TitleThe structure of DcsB complex with its substrate analogue
ComponentsDltD domain-containing protein
KeywordsHYDROLASE / Thioesterase / Complex
Function / homologySerine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / Chem-GY0 / methyl 3-sulfanylpropanoate / DltD domain-containing protein
Function and homology information
Biological speciesBeauveria bassiana
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.10411425302 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)141,83919
Polymers140,6934
Non-polymers1,14615
Water10,323573
1
D: DltD domain-containing protein
A: DltD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,16012
Polymers70,3472
Non-polymers81310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-16 kcal/mol
Surface area21520 Å2
MethodPISA
2
C: DltD domain-containing protein
hetero molecules

B: DltD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6797
Polymers70,3472
Non-polymers3335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4790 Å2
ΔGint-45 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.263, 59.011, 113.990
Angle α, β, γ (deg.)84.846, 78.552, 84.008
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 4 molecules DABC

#1: Protein
DltD domain-containing protein / Thioesterase


Mass: 35173.262 Da / Num. of mol.: 4
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 , 7 types, 588 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GY0 / methyl 3-[(E,3R,9R)-3,9-bis(oxidanyl)dec-4-enoyl]sulfanylpropanoate


Mass: 304.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H24O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GYF / methyl 3-sulfanylpropanoate


Mass: 120.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 289.2 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M MMT, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 64129 / % possible obs: 92.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.6699461815 Å2 / CC1/2: 0.75 / Net I/σ(I): 9.56
Reflection shellResolution: 2.11→2.15 Å / Num. unique obs: 64129 / CC1/2: 0.734

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.10411425302→39.0031543568 Å / SU ML: 0.265288513473 / Cross valid method: FREE R-VALUE / σ(F): 1.97263301931 / Phase error: 24.2618528783
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.226936694139 2979 4.98794454491 %
Rwork0.182374770165 56745 -
obs0.184609801223 59724 85.9610236334 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.1019481266 Å2
Refinement stepCycle: LAST / Resolution: 2.10411425302→39.0031543568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8978 0 68 573 9619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00188446566649261
X-RAY DIFFRACTIONf_angle_d0.48935190025112509
X-RAY DIFFRACTIONf_chiral_restr0.04357970862751379
X-RAY DIFFRACTIONf_plane_restr0.00389818491591634
X-RAY DIFFRACTIONf_dihedral_angle_d3.012531370347272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.13860.321349440053890.2426155297571673X-RAY DIFFRACTION53.7686908758
2.1386-2.17550.2533415400621130.2164536925262000X-RAY DIFFRACTION63.5871200722
2.1755-2.2150.2687058398481190.2265060945842190X-RAY DIFFRACTION69.9696969697
2.215-2.25760.3329954083831160.2468695187182371X-RAY DIFFRACTION74.2388059701
2.2576-2.30370.3009265876361350.2172181129152474X-RAY DIFFRACTION80.006133088
2.3037-2.35380.3169919402511230.207945007812715X-RAY DIFFRACTION85.071942446
2.3538-2.40850.254573891741270.2076577332882708X-RAY DIFFRACTION86.7237687366
2.4085-2.46880.269986044071540.2065219788062752X-RAY DIFFRACTION86.1292234736
2.4688-2.53550.249126095511320.2039854230852770X-RAY DIFFRACTION89.3748075146
2.5355-2.61010.2863934872581560.2007106024972998X-RAY DIFFRACTION94.601079784
2.6101-2.69430.2436096214791810.1994336920342932X-RAY DIFFRACTION94.9085365854
2.6943-2.79060.2577414490841660.2036820132942988X-RAY DIFFRACTION93.9529341674
2.7906-2.90230.2397136970991510.1987809438822927X-RAY DIFFRACTION94.3014705882
2.9023-3.03430.2631010443841440.2025240189722940X-RAY DIFFRACTION93.0036188179
3.0343-3.19420.2564093739031240.1946422509592813X-RAY DIFFRACTION88.7311178248
3.1942-3.39430.2200371534321600.1899275160642862X-RAY DIFFRACTION91.216420163
3.3943-3.65620.185548695341580.1745930102413044X-RAY DIFFRACTION96.0696069607
3.6562-4.02380.2092131990151670.1570583053052933X-RAY DIFFRACTION94.7722409049
4.0238-4.60520.1684922861951360.145233194972887X-RAY DIFFRACTION90.7535274692
4.6052-5.7990.1939123812151630.153130658152915X-RAY DIFFRACTION92.8226779252
5.799-5.7990.1861326772311650.1537254710882853X-RAY DIFFRACTION91.3438256659

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