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- PDB-3hrq: The Product Template Domain from PksA with palmitate bound -

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Basic information

Entry
Database: PDB / ID: 3hrq
TitleThe Product Template Domain from PksA with palmitate bound
ComponentsAflatoxin biosynthesis polyketide synthase
KeywordsBIOSYNTHETIC PROTEIN / hot-dog fold / PksA / polyketide synthase / iterative Type I PKS / aflatoxin / norsolorinic acid / product template domain / Acyltransferase / Multifunctional enzyme / Phosphopantetheine
Function / homology
Function and homology information


noranthrone synthase / aflatoxin biosynthetic process / norsolorinate anthrone synthase activity / fatty acid synthase activity / phosphopantetheine binding / fatty acid biosynthetic process / identical protein binding
Similarity search - Function
Polyketide product template domain / Polyketide synthase dehydratase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / : / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Thioesterase / Thioesterase domain / Polyketide synthase dehydratase N-terminal domain ...Polyketide product template domain / Polyketide synthase dehydratase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / : / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Thioesterase / Thioesterase domain / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain superfamily / Thiol Ester Dehydrase; Chain A / 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 / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / Roll / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Norsolorinic acid synthase
Similarity search - Component
Biological speciesAspergillus parasiticus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsKorman, T.P. / Tsai, S.C.
CitationJournal: Nature / Year: 2009
Title: Structural basis for biosynthetic programming of fungal aromatic polyketide cyclization.
Authors: Crawford, J.M. / Korman, T.P. / Labonte, J.W. / Vagstad, A.L. / Hill, E.A. / Kamari-Bidkorpeh, O. / Tsai, S.C. / Townsend, C.A.
History
DepositionJun 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Aflatoxin biosynthesis polyketide synthase
B: Aflatoxin biosynthesis polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2624
Polymers78,7492
Non-polymers5132
Water8,251458
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aflatoxin biosynthesis polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6312
Polymers39,3751
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Aflatoxin biosynthesis polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6312
Polymers39,3751
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.793, 91.247, 91.233
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aflatoxin biosynthesis polyketide synthase / PKS


Mass: 39374.738 Da / Num. of mol.: 2 / Fragment: UNP residues 1305-1660
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus parasiticus (mold) / Gene: PksA, pksL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12053
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.22 M Ammonium Acetate, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98, 0.96482, 0.98025
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2007
Details: Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal; asymmetric cut 12.2 degs
Protocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.964821
30.980251
ReflectionResolution: 1.8→50 Å / Num. obs: 69471 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.049 / Χ2: 1.115 / Net I/σ(I): 43.697
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.867.40.40868721.168100
1.86-1.947.40.29668511.237100
1.94-2.037.50.20668641.157100
2.03-2.137.50.14268661.103100
2.13-2.277.50.10569161.059100
2.27-2.447.50.08568871.058100
2.44-2.697.50.0769501.096100
2.69-3.087.50.04669770.952100
3.08-3.887.50.02770061.167100
3.88-507.20.02272821.15999.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→37.08 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.223 6805 9.8 %
Rwork0.203 --
obs-67206 97 %
Solvent computationBsol: 53.365 Å2
Displacement parametersBiso max: 75.32 Å2 / Biso mean: 27.036 Å2 / Biso min: 9.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.358 Å20 Å20 Å2
2--0.649 Å20 Å2
3---0.709 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4961 0 36 458 5455
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.281
X-RAY DIFFRACTIONc_mcbond_it1.4611.5
X-RAY DIFFRACTIONc_scbond_it2.1382
X-RAY DIFFRACTIONc_mcangle_it2.4062
X-RAY DIFFRACTIONc_scangle_it3.2072.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5plm.parplm.top

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