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- PDB-8avz: Crystal structure of PksD, the trans-acting acyl hydrolase domain... -

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Basic information

Entry
Database: PDB / ID: 8avz
TitleCrystal structure of PksD, the trans-acting acyl hydrolase domain from the bacillaene trans-AT PKS (SeMet derivative)
ComponentsPolyketide biosynthesis acyltransferase homolog PksD
KeywordsHYDROLASE / alpha/beta-hydrolase / acyltransferase / polyketide synthase / biosynthesis
Function / homology
Function and homology information


acyltransferase activity / antibiotic biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytoplasm
Similarity search - Function
Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase
Similarity search - Domain/homology
Polyketide biosynthesis acyltransferase homolog PksD
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å
AuthorsFage, C.D. / Challis, G.L. / Lewandowski, J. / Jenner, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Structural basis for acyl hydrolysis in trans-AT polyketide synthases
Authors: Fage, C.D. / Passmore, M. / Tatman, B. / Smith, H.G. / Jian, X. / Mudiyanselage, U.C.M. / Berger, M. / Cisneros, A.G. / Challis, G.L. / Lewandowski, J.R. / Jenner, M.
History
DepositionAug 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyketide biosynthesis acyltransferase homolog PksD
B: Polyketide biosynthesis acyltransferase homolog PksD
C: Polyketide biosynthesis acyltransferase homolog PksD
D: Polyketide biosynthesis acyltransferase homolog PksD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,9286
Polymers150,7974
Non-polymers1312
Water12,088671
1
A: Polyketide biosynthesis acyltransferase homolog PksD
C: Polyketide biosynthesis acyltransferase homolog PksD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4643
Polymers75,3982
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-42 kcal/mol
Surface area25810 Å2
MethodPISA
2
B: Polyketide biosynthesis acyltransferase homolog PksD
D: Polyketide biosynthesis acyltransferase homolog PksD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4643
Polymers75,3982
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-43 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.708, 83.564, 145.742
Angle α, β, γ (deg.)90.000, 119.710, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Polyketide biosynthesis acyltransferase homolog PksD / AT / Transacylase


Mass: 37699.199 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: PksD, with an N-terminal Gly-Ser-His thrombin cleavage scar
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: pksD, BSU17110 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O34877, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 671 / Source method: isolated from a natural source / Formula: H2O
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: 3.7 Å3/Da / Density % sol: 66.74 % / Description: Rectangular prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 7% (w/v) PEG 8000; streak-seeded with native crystals

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 1.96→90.2 Å / Num. obs: 155431 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 37.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.034 / Rrim(I) all: 0.125 / Net I/σ(I): 13.6 / Num. measured all: 2104939 / Scaling rejects: 137
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.96-1.9912.92.3869837576390.6750.6882.4851.2100
10.74-90.2130.0571333910230.9990.0160.0640.699.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.27data extraction
PHENIX1.19.2-4158refinement
PHENIX1.14phasing
Aimless1.12.2data scaling
XDSMar 15, 2019data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.96→59.79 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 7694 4.96 %RANDOM
Rwork0.1786 147478 --
obs0.1798 155172 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.46 Å2 / Biso mean: 47.8912 Å2 / Biso min: 24.63 Å2
Refinement stepCycle: final / Resolution: 1.96→59.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10034 0 2 671 10707
Biso mean--45.04 54.4 -
Num. residues----1262
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.96-1.980.4422680.398348425110100
1.98-2.010.33522410.364748805121100
2.01-2.030.38392540.348249355189100
2.03-2.060.37792830.339448495132100
2.06-2.080.35882560.322449165172100
2.08-2.110.32852670.28948695136100
2.11-2.140.31142730.270648845157100
2.14-2.170.30182300.252348725102100
2.17-2.210.28652550.246949595214100
2.21-2.240.28292570.259748345091100
2.24-2.280.26632480.219249035151100
2.28-2.320.24182530.20549215174100
2.32-2.370.25482560.198148685124100
2.37-2.420.21832750.191948845159100
2.42-2.470.22272370.19249505187100
2.47-2.530.2252450.19348925137100
2.53-2.590.22962600.194949265186100
2.59-2.660.23522620.192649075169100
2.66-2.740.20652510.184349325183100
2.74-2.830.20412640.180248655129100
2.83-2.930.22182650.185649245189100
2.93-3.040.22072550.178349335188100
3.05-3.180.2062380.177149555193100
3.18-3.350.18962610.170649315192100
3.35-3.560.18732370.15949535190100
3.56-3.840.16262670.15149475214100
3.84-4.220.17392530.137249335186100
4.22-4.830.14122650.127849785243100
4.83-6.090.16632660.148949835249100
6.09-59.790.16252520.16585053530599

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