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- PDB-4xs7: Determining the Molecular Basis for Starter Unit Selection During... -

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Basic information

Entry
Database: PDB / ID: 4xs7
TitleDetermining the Molecular Basis for Starter Unit Selection During Daunorubicin Biosynthesis
ComponentsDaunorubicin-doxorubicin polyketide synthase
KeywordsTRANSFERASE / polyketide / daunrubicin / 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: 2.4 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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)78,9452
Polymers78,9452
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-37 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.213, 91.213, 315.643
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: 39472.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Serine 118 is modified to an acetyl-serine residue / 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.: 248 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.76 %
Description: hexagonal crystals that look 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: 0.97753 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97753 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 31503 / % possible obs: 100 % / Redundancy: 15.9 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 18.6
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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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: 2.4→49.315 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 1999 6.37 %
Rwork0.177 --
obs0.1794 31387 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→49.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5068 0 0 248 5316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095209
X-RAY DIFFRACTIONf_angle_d1.1257099
X-RAY DIFFRACTIONf_dihedral_angle_d14.1741839
X-RAY DIFFRACTIONf_chiral_restr0.069773
X-RAY DIFFRACTIONf_plane_restr0.005941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.46040.2651330.20061953X-RAY DIFFRACTION97
2.4604-2.52690.34261390.21952045X-RAY DIFFRACTION100
2.5269-2.60120.31381400.21712062X-RAY DIFFRACTION100
2.6012-2.68520.28531410.22322073X-RAY DIFFRACTION100
2.6852-2.78120.2731390.22482048X-RAY DIFFRACTION100
2.7812-2.89250.27241400.2222054X-RAY DIFFRACTION100
2.8925-3.02410.26431410.20622079X-RAY DIFFRACTION100
3.0241-3.18350.24761420.19722079X-RAY DIFFRACTION100
3.1835-3.38290.21541420.18492095X-RAY DIFFRACTION100
3.3829-3.64410.22141430.17542105X-RAY DIFFRACTION100
3.6441-4.01060.17821440.14942120X-RAY DIFFRACTION100
4.0106-4.59060.18141460.13622138X-RAY DIFFRACTION100
4.5906-5.78230.17721490.15072181X-RAY DIFFRACTION100
5.7823-49.32550.17981600.17912356X-RAY DIFFRACTION100

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