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- PDB-3hrr: The Product Template Domain from PksA with Harris Compound Bound -

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Basic information

Entry
Database: PDB / ID: 3hrr
TitleThe Product Template Domain from PksA with Harris Compound Bound
ComponentsAflatoxin biosynthesis polyketide synthase
KeywordsTRANSCRIPTION / PksA / aflatoxin / norsolorinic acid / polyketide / polyketide synthase / PKS / iterative Type I PKS / Harris Compound / hot-dog fold / Acyltransferase / Multifunctional enzyme / Phosphopantetheine / Transferase
Function / homology
Function and homology information


noranthrone synthase / aflatoxin biosynthetic process / norsolorinate anthrone synthase activity / phosphopantetheine binding / 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 synthase, dehydratase domain superfamily ...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
Chem-HC8 / Norsolorinic acid synthase
Similarity search - Component
Biological speciesAspergillus parasiticus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)79,0644
Polymers78,4872
Non-polymers5772
Water7,062392
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)39,5322
Polymers39,2441
Non-polymers2881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Aflatoxin biosynthesis polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5322
Polymers39,2441
Non-polymers2881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.809, 90.609, 90.660
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: 39243.543 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-HC8 / 1-(3-acetyl-4,5-dihydroxy-7-methoxynaphthalen-2-yl)propan-2-one


Mass: 288.295 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
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: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 4, 2008
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: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 58378 / Num. obs: 57678 / % possible obs: 98.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.06 / Χ2: 0.987 / Net I/σ(I): 30.643
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.975.10.28951590.94989.7
1.97-2.056.50.23356870.98498.6
2.05-2.147.30.18357340.972100
2.14-2.257.40.14257831.034100
2.25-2.397.40.11857970.969100
2.39-2.587.40.09958050.949100
2.58-2.847.40.0858350.98999.9
2.84-3.257.30.06858340.99499.9
3.25-4.097.10.04359030.92799.9
4.09-5070.02761411.082100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HRQ

3hrq


Resolution: 1.9→44.4 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.867 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2916 5.1 %RANDOM
Rwork0.19 ---
obs0.192 57591 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.51 Å2 / Biso mean: 25.291 Å2 / Biso min: 8.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2--0.41 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4954 0 42 392 5388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225097
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9596901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9795627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66323.652230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61915862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4421536
X-RAY DIFFRACTIONr_chiral_restr0.1050.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023834
X-RAY DIFFRACTIONr_nbd_refined0.2130.22344
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23440
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2406
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.225
X-RAY DIFFRACTIONr_mcbond_it1.1721.53239
X-RAY DIFFRACTIONr_mcangle_it1.89925071
X-RAY DIFFRACTIONr_scbond_it2.65132159
X-RAY DIFFRACTIONr_scangle_it4.3324.51830
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 162 -
Rwork0.222 3559 -
all-3721 -
obs--87.78 %

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