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- PDB-4ku3: Crystal Structure of C143S Xanthomonas Campestris OleA bound with... -

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Basic information

Entry
Database: PDB / ID: 4ku3
TitleCrystal Structure of C143S Xanthomonas Campestris OleA bound with myristic acid and myrisotoyl-CoA
Components3-oxoacyl-[ACP] synthase III
KeywordsTRANSFERASE / Thiolase
Function / homology
Function and homology information


acyl-CoA:acyl-CoA alkyltransferase / secondary metabolite biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
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
TETRADECANOYL-COA / MYRISTIC ACID / DI(HYDROXYETHYL)ETHER / Acyl-CoA:acyl-CoA alkyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.97 Å
AuthorsGoblirsch, B.R.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Substrate Trapping in Crystals of the Thiolase OleA Identifies Three Channels That Enable Long Chain Olefin Biosynthesis.
Authors: Goblirsch, B.R. / Jensen, M.R. / Mohamed, F.A. / Wackett, L.P. / Wilmot, C.M.
History
DepositionMay 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 3-oxoacyl-[ACP] synthase III
B: 3-oxoacyl-[ACP] synthase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0716
Polymers77,6532
Non-polymers1,4194
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-16 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.204, 85.379, 102.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-oxoacyl-[ACP] synthase III


Mass: 38826.379 Da / Num. of mol.: 2 / Mutation: C143S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: ATCC 33913 / NCPPB 528 / LMG 568 / Gene: fabH, XCC0212 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PDX2
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#4: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 15% PEG 8000, 80 mM potassium phosphate dibasic, 100 mM sodium citrate , pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 4, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. all: 390033 / Num. obs: 51928 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 23.9
Reflection shellResolution: 1.97→2 Å / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3ROW

3row


Resolution: 1.97→44.006 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1962 2608 5.03 %
Rwork0.1544 --
obs0.1565 51853 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.97→44.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5138 0 93 461 5692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015380
X-RAY DIFFRACTIONf_angle_d1.2027296
X-RAY DIFFRACTIONf_dihedral_angle_d15.772010
X-RAY DIFFRACTIONf_chiral_restr0.082850
X-RAY DIFFRACTIONf_plane_restr0.005938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9439-1.97920.3233460.1852816X-RAY DIFFRACTION31
1.9792-2.01730.27241340.20772589X-RAY DIFFRACTION98
2.0173-2.05850.27031450.19122673X-RAY DIFFRACTION100
2.0585-2.10330.25441460.17932624X-RAY DIFFRACTION100
2.1033-2.15220.21831310.17342693X-RAY DIFFRACTION100
2.1522-2.2060.23021470.15832642X-RAY DIFFRACTION100
2.206-2.26560.24251370.16762654X-RAY DIFFRACTION100
2.2656-2.33230.21841380.16532676X-RAY DIFFRACTION100
2.3323-2.40760.23141400.17292671X-RAY DIFFRACTION100
2.4076-2.49360.24821550.16832667X-RAY DIFFRACTION100
2.4936-2.59350.22371390.16752668X-RAY DIFFRACTION100
2.5935-2.71150.21321400.15872675X-RAY DIFFRACTION100
2.7115-2.85440.20741470.16342708X-RAY DIFFRACTION100
2.8544-3.03320.20141390.17042704X-RAY DIFFRACTION100
3.0332-3.26730.21891400.17522695X-RAY DIFFRACTION100
3.2673-3.5960.18751430.15252710X-RAY DIFFRACTION100
3.596-4.1160.16751470.1332740X-RAY DIFFRACTION100
4.116-5.18440.16771420.11752752X-RAY DIFFRACTION100
5.1844-44.01750.13871520.14632888X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9123-0.17120.21931.59460.0660.5367-0.0652-0.0745-0.02730.17720.01280.07840.1072-0.04670.04960.1837-0.02810.0570.1729-0.00520.1414-10.63986.7333-2.9725
20.77180.1226-0.37512.05980.32471.7774-0.03340.13580.0072-0.6045-0.02390.16580.0107-0.07660.04750.3069-0.0263-0.01830.19890.01120.1893-12.320824.0193-27.7246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 20:358)
2X-RAY DIFFRACTION2(chain B and resid 22:358)

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