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

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Basic information

Entry
Database: PDB / ID: 4xsa
TitleDetermining the Molecular Basis for Starter Unit Selection During Daunorubicin Biosynthesis
ComponentsDaunorubicin-doxorubicin polyketide synthase
KeywordsTRANSFERASE / biosynthesis / polyketide / daunorubicin / 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
Daunorubicin-doxorubicin polyketide synthase
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Daunorubicin-doxorubicin polyketide synthase
B: Daunorubicin-doxorubicin polyketide synthase


Theoretical massNumber of molelcules
Total (without water)78,9732
Polymers78,9732
Non-polymers00
Water10,305572
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-32 kcal/mol
Surface area23400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.476, 91.476, 316.834
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Daunorubicin-doxorubicin polyketide synthase / DpsC


Mass: 39486.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Serine 118 is modified to propionyl-serine / Source: (gene. exp.) Streptomyces peucetius (bacteria) / Gene: dpsC / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q54816, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Description: hexagonal crystals that looked 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: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40753 / % possible obs: 99.6 % / Redundancy: 21 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 22.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 20.2 % / Rmerge(I) obs: 0.759 / % possible all: 99.2

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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: 2.204→45.738 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2029 2000 4.92 %
Rwork0.1664 --
obs0.1681 40679 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.204→45.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5102 0 0 572 5674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075233
X-RAY DIFFRACTIONf_angle_d1.0687132
X-RAY DIFFRACTIONf_dihedral_angle_d13.491848
X-RAY DIFFRACTIONf_chiral_restr0.07776
X-RAY DIFFRACTIONf_plane_restr0.005946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.204-2.25880.22591380.17192666X-RAY DIFFRACTION99
2.2588-2.31980.21961380.18452682X-RAY DIFFRACTION99
2.3198-2.38810.23351400.18032698X-RAY DIFFRACTION99
2.3881-2.46520.2161410.1822725X-RAY DIFFRACTION100
2.4652-2.55330.23741400.18312705X-RAY DIFFRACTION100
2.5533-2.65550.18651390.1782691X-RAY DIFFRACTION100
2.6555-2.77630.26561410.18612730X-RAY DIFFRACTION100
2.7763-2.92270.22161410.17252729X-RAY DIFFRACTION100
2.9227-3.10570.19851430.1752767X-RAY DIFFRACTION100
3.1057-3.34550.22311420.16912745X-RAY DIFFRACTION100
3.3455-3.6820.18951460.15532803X-RAY DIFFRACTION100
3.682-4.21450.16351440.14632800X-RAY DIFFRACTION100
4.2145-5.30850.16231480.13482877X-RAY DIFFRACTION100
5.3085-45.74780.21311590.1823061X-RAY DIFFRACTION100

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