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- PDB-8aw0: Crystal structure of PksD, the trans-acting acyl hydrolase domain... -

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Basic information

Entry
Database: PDB / ID: 8aw0
TitleCrystal structure of PksD, the trans-acting acyl hydrolase domain from the bacillaene trans-AT PKS (native)
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 / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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: Jacs Au / Year: 2025
Title: Molecular Basis for Short-Chain Thioester Hydrolysis by Acyl Hydrolases in trans-Acyltransferase Polyketide Synthases
Authors: Fage, C.D. / Passmore, M. / Tatman, B.P. / Smith, H.G. / Jian, X. / Dissanayake, U.C. / Foran, M.E. / Cisneros, G.A. / 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
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Nov 27, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _pdbx_entry_details.has_protein_modification
Revision 1.3Feb 5, 2025Group: Database references / Category: citation / pdbx_database_related / Item: _citation.year

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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
E: Polyketide biosynthesis acyltransferase homolog PksD
F: Polyketide biosynthesis acyltransferase homolog PksD
G: Polyketide biosynthesis acyltransferase homolog PksD
H: Polyketide biosynthesis acyltransferase homolog PksD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,35312
Polymers297,0928
Non-polymers2624
Water10,034557
1
A: Polyketide biosynthesis acyltransferase homolog PksD
F: Polyketide biosynthesis acyltransferase homolog PksD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3383
Polymers74,2732
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-44 kcal/mol
Surface area26670 Å2
MethodPISA
2
B: Polyketide biosynthesis acyltransferase homolog PksD
D: Polyketide biosynthesis acyltransferase homolog PksD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3383
Polymers74,2732
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-45 kcal/mol
Surface area26280 Å2
MethodPISA
3
C: Polyketide biosynthesis acyltransferase homolog PksD
H: Polyketide biosynthesis acyltransferase homolog PksD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3383
Polymers74,2732
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-43 kcal/mol
Surface area26510 Å2
MethodPISA
4
E: Polyketide biosynthesis acyltransferase homolog PksD
hetero molecules

G: Polyketide biosynthesis acyltransferase homolog PksD


Theoretical massNumber of molelcules
Total (without water)74,3383
Polymers74,2732
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1110 Å2
ΔGint-45 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.202, 163.330, 186.871
Angle α, β, γ (deg.)90.000, 104.500, 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: 37136.457 Da / Num. of mol.: 8
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.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.76 Å3/Da / Density % sol: 67.28 % / Description: Rectangular prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.2→90.46 Å / Num. obs: 220807 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 15.2 / Num. measured all: 1524232 / Scaling rejects: 4
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
2.2-2.244.72.81547635100690.2231.4113.1660.591.6
12.05-90.4670.019982214100.9990.0080.02172.299.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.69 Å90.46 Å
Translation3.69 Å90.46 Å

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.27data extraction
PHENIX1.18.2-3874refinement
PHASER2.8.3phasing
Aimless0.7.4data scaling
XDSMar 15, 2019data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet-derived PksD

Resolution: 2.2→51.08 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 11227 5.1 %
Rwork0.1978 208980 -
obs0.1993 220207 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.93 Å2 / Biso mean: 75.4819 Å2 / Biso min: 40.49 Å2
Refinement stepCycle: final / Resolution: 2.2→51.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20149 0 4 557 20710
Biso mean--75.61 77.43 -
Num. residues----2534
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 (%)
2.2-2.230.47583410.46885985632685
2.23-2.250.44713500.43316663701395
2.25-2.280.43513730.40246920729399
2.28-2.310.41583800.383269867366100
2.31-2.340.42223640.370169597323100
2.34-2.370.39333920.352670537445100
2.37-2.40.35273940.329469007294100
2.4-2.440.35893650.315370077372100
2.44-2.480.33593960.300770217417100
2.48-2.520.34323800.293769437323100
2.52-2.560.33253660.291570287394100
2.56-2.610.31683550.283270147369100
2.61-2.660.29913510.26570237374100
2.66-2.710.29913890.248570407429100
2.71-2.770.30823480.248669777325100
2.77-2.840.30133810.247469997380100
2.84-2.910.2833880.24170267414100
2.91-2.990.27733740.234369667340100
2.99-3.070.26733600.230670537413100
3.07-3.170.28463930.237270157408100
3.17-3.290.25533930.21970047397100
3.29-3.420.23953730.208269657338100
3.42-3.570.22693630.203770697432100
3.57-3.760.23543710.196770147385100
3.76-40.19473790.17370447423100
4-4.310.19133860.155570207406100
4.31-4.740.17523960.145470107406100
4.74-5.420.16623950.153570287423100
5.42-6.830.19923460.176871287474100
6.83-51.080.16733850.14827120750599

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