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- PDB-5vxh: Crystal structure of Xanthomonas campestris OleA E117D -

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Basic information

Entry
Database: PDB / ID: 5vxh
TitleCrystal structure of Xanthomonas campestris OleA E117D
Components3-oxoacyl-[ACP] synthase III
KeywordsTRANSFERASE / Thiolase / Condensation
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
PHOSPHATE ION / Acyl-CoA:acyl-CoA alkyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.84 Å
AuthorsJensen, M.R. / Wilmot, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-008700 United States
CitationJournal: Biochem. J. / Year: 2017
Title: OleA Glu117 is key to condensation of two fatty-acyl coenzyme A substrates in long-chain olefin biosynthesis.
Authors: Jensen, M.R. / Goblirsch, B.R. / Christenson, J.K. / Esler, M.A. / Mohamed, F.A. / Wackett, L.P. / Wilmot, C.M.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

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)78,1207
Polymers77,6572
Non-polymers4635
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, OleA elutes as a dimer through gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-19 kcal/mol
Surface area25250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.876, 85.409, 102.794
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 38828.418 Da / Num. of mol.: 2 / Mutation: E117D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25) (bacteria)
Strain: ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25 / Gene: fabH, XCC0212 / Plasmid: pET28b+ / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8PDX2, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.4 Å3/Da / Density % sol: 48.8 % / Mosaicity: 0.491 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 14% PEG 8000, 100 mM potassium phosphate dibasic, 100 mM sodium citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.02235 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02235 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 63324 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Χ2: 1.081 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.84-1.876.90.9750.7360.41.292100
1.87-1.917.40.8780.8020.3481.2841000.945
1.91-1.947.40.6990.8640.2761.2551000.753
1.94-1.987.40.5670.8890.2231.2051000.609
1.98-2.037.40.4940.9080.1951.1691000.532
2.03-2.077.40.4140.9380.1631.1481000.445
2.07-2.127.40.3360.9570.1331.0661000.362
2.12-2.187.40.2780.9690.111.1611000.299
2.18-2.257.40.2410.9780.0951.1281000.259
2.25-2.327.40.210.9830.0831.0781000.226
2.32-2.47.40.1920.9850.0761.0471000.207
2.4-2.57.40.1590.9890.0630.9991000.171
2.5-2.617.40.1330.9910.0520.951000.143
2.61-2.757.40.1110.9940.0441.0491000.12
2.75-2.927.40.0890.9970.0351.0281000.096
2.92-3.157.40.0710.9970.0281.0611000.077
3.15-3.467.40.0540.9980.0211.0141000.058
3.46-3.967.30.0410.9990.0160.9331000.044
3.96-4.997.20.0310.9990.0120.8731000.034
4.99-506.70.0340.9990.0150.90899.50.037

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Processing

Software
NameVersionClassification
HKL-2000v705data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
REFMAC5.8.0158phasing
HKLdata scaling
HKL-2000v705data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3ROW

3row


Resolution: 1.84→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.219 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3170 5 %RANDOM
Rwork0.1582 ---
obs0.1602 60084 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.15 Å2 / Biso mean: 28.939 Å2 / Biso min: 14.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-0 Å2
2---1.06 Å2-0 Å2
3---0.2 Å2
Refinement stepCycle: final / Resolution: 1.84→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5093 0 29 226 5348
Biso mean--42.48 31.02 -
Num. residues----671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0195275
X-RAY DIFFRACTIONr_bond_other_d0.0020.025066
X-RAY DIFFRACTIONr_angle_refined_deg2.4481.9677153
X-RAY DIFFRACTIONr_angle_other_deg1.226311714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6435686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86824.194217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83215917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1321537
X-RAY DIFFRACTIONr_chiral_restr0.170.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025896
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021025
LS refinement shellResolution: 1.839→1.887 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 233 -
Rwork0.218 4377 -
all-4610 -
obs--99.48 %
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)
10.4329-0.13820.10070.34880.06980.1413-0.0215-0.022-0.0450.06670.0160.04770.03530.00170.00550.023-0.0040.01470.02620.0040.0171-10.97617.0358-2.2921
20.20220.0147-0.2080.415-0.11730.62270.01380.02070.0038-0.1255-0.022-0.00070.0453-0.04620.00820.05470.00510.00160.0221-0.0020.0006-13.558724.2128-27.2667
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 358
2X-RAY DIFFRACTION2B21 - 358

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