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- PDB-1mzj: Crystal Structure of the Priming beta-Ketosynthase from the R1128... -

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Basic information

Entry
Database: PDB / ID: 1mzj
TitleCrystal Structure of the Priming beta-Ketosynthase from the R1128 Polyketide Biosynthetic Pathway
ComponentsBeta-ketoacylsynthase III
KeywordsTRANSFERASE / beta-Ketosynthase / aromatic polyketide / biosynthetic engineering / catalytic triad
Function / homology
Function and homology information


branched-chain beta-ketoacyl-[acyl-carrier-protein] synthase / beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / secondary metabolite biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 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
ACETYL GROUP / COENZYME A / Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesStreptomyces sp. R1128 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPan, H. / Tsai, S.C. / Meadows, E.S. / Miercke, L.J.W. / Keatinge-Clay, A. / O'Connell, J. / Khosla, C. / Stroud, R.M.
CitationJournal: Structure
Title: Crystal structure of the priming beta-ketosynthase from the R1128 polyketide biosynthetic pathway
Authors: Pan, H. / Tsai, S. / Meadows, E.S. / Miercke, L.J. / Keatinge-Clay, A.T. / O'Connell, J. / Khosla, C. / Stroud, R.M.
History
DepositionOct 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Beta-ketoacylsynthase III
B: Beta-ketoacylsynthase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4796
Polymers70,8562
Non-polymers1,6234
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-35 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.000, 96.000, 72.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Beta-ketoacylsynthase III / beta-ketosynthase


Mass: 35428.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. R1128 (bacteria) / Gene: zhuH / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9F6D4, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 8000, sodium cacodylate, magnesium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 mg/mlprotein1drop
210 mMTris1droppH7.4
31 mMdithiothreitol1drop
410 %(w/v)PEG80001reservoir
5200 mMmagnesium acetate1reservoir
6100 mMsodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2000 / Details: Flat mirror + single crystal Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 43722 / Num. obs: 43722 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.057 / Rsym value: 0.055 / Net I/σ(I): 8.6
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3 / Num. unique all: 2231 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 40 Å / Redundancy: 6.1 % / Num. measured all: 264571 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EBL

1ebl


Resolution: 2.1→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2186 -random
Rwork0.215 ---
all0.217 43722 --
obs0.217 43722 99.5 %-
Refinement stepCycle: LAST / Resolution: 2.1→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4909 0 102 379 5390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.006
X-RAY DIFFRACTIONc_angle_deg1.67
Refinement
*PLUS
Num. reflection obs: 41952
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d

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