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- PDB-4xs9: Determining the Molecular Basis for Starter Unit Selection During... -

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Basic information

Entry
Database: PDB / ID: 4xs9
TitleDetermining the Molecular Basis for Starter Unit Selection During Daunorubicin Biosynthesis
ComponentsDaunorubicin-doxorubicin polyketide synthase
KeywordsTRANSFERASE / polyketide / daunorubicin / natural product / starter unit
Function / homology
Function and homology information


secondary metabolite biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-42X / Daunorubicin-doxorubicin polyketide synthase
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsJackson, D.R. / Valentic, T.R. / Tsai, S.C. / Patel, A. / Mohammed, L. / Vasilakis, K. / Wattana-amorn, P. / Long, P.F. / Crump, M.P. / Crosby, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM100305-03 United States
CitationJournal: To Be Published
Title: Determining the Molecular Basis for Starter Unit Selection During Daunorubicin Biosynthesis
Authors: Jackson, D.R. / Valentic, T.R. / Tsai, S.C. / Patel, A. / Mohammed, L. / Vasilakis, K. / Wattana-amorn, P. / Long, P.F. / Crump, M.P. / Crosby, J.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Daunorubicin-doxorubicin polyketide synthase
B: Daunorubicin-doxorubicin polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6564
Polymers78,8612
Non-polymers7952
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-36 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.798, 89.798, 303.038
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-523-

HOH

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Components

#1: Protein Daunorubicin-doxorubicin polyketide synthase / DpsC


Mass: 39430.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein was co-crystallized with a propionyl phosphopantetheine analogue
Source: (gene. exp.) Streptomyces peucetius (bacteria) / Gene: dpsC / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: Q54816, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-42X / N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-[2-(propanoylamino)ethyl]-beta-alaninamide


Mass: 397.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28N3O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 % / Description: hexagonal crystals shaped like Monopoly houses
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.18 M sodium citrate, 26% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→38.88 Å / Num. obs: 49899 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 18.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 1.75 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4XQP

4xqp
PDB Unreleased entry


Resolution: 2.002→38.88 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1913 2000 4.02 %
Rwork0.1707 --
obs0.1715 49779 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.002→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5069 0 52 435 5556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075254
X-RAY DIFFRACTIONf_angle_d1.0827161
X-RAY DIFFRACTIONf_dihedral_angle_d13.8791867
X-RAY DIFFRACTIONf_chiral_restr0.072776
X-RAY DIFFRACTIONf_plane_restr0.005945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.05250.32241380.2683311X-RAY DIFFRACTION100
2.0525-2.1080.2631400.23343328X-RAY DIFFRACTION100
2.108-2.170.24851390.21233327X-RAY DIFFRACTION100
2.17-2.240.22711420.19123372X-RAY DIFFRACTION100
2.24-2.32010.21971390.18343347X-RAY DIFFRACTION100
2.3201-2.4130.19811410.17693358X-RAY DIFFRACTION100
2.413-2.52280.20741400.17713360X-RAY DIFFRACTION100
2.5228-2.65570.19231430.17523394X-RAY DIFFRACTION100
2.6557-2.82210.20881410.17863387X-RAY DIFFRACTION100
2.8221-3.03990.22961430.1793404X-RAY DIFFRACTION100
3.0399-3.34570.20061440.16883433X-RAY DIFFRACTION100
3.3457-3.82940.15261450.15283461X-RAY DIFFRACTION100
3.8294-4.82320.16761470.13863529X-RAY DIFFRACTION100
4.8232-38.8910.16971580.17463768X-RAY DIFFRACTION100

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