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- PDB-5vxd: Crystal structure of Xanthomonas campestris OleA E117A -

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Basic information

Entry
Database: PDB / ID: 5vxd
TitleCrystal structure of Xanthomonas campestris OleA E117A
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
Acyl-CoA:acyl-CoA alkyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.968 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)77,7534
Polymers77,5692
Non-polymers1842
Water3,207178
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 area5230 Å2
ΔGint-11 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.393, 85.988, 103.562
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: 38784.406 Da / Num. of mol.: 2 / Mutation: E117A
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(DE3) (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.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.45 Å3/Da / Density % sol: 49.89 % / Mosaicity: 0.262 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 16% PEG 8000, 105 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: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 30, 2014
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 52682 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 26.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.058 / Rrim(I) all: 0.117 / Χ2: 1.068 / Net I/av σ(I): 11.8 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.968-1.9940.714225990.5810.4140.8271.073100
1.99-2.0340.62125930.6560.360.721.07100
2.03-2.0740.53125910.7380.3070.6151.19100
2.07-2.1140.41625970.8140.2410.4831.098100
2.11-2.1640.34126320.870.1960.3941.095100
2.16-2.2140.29525850.9050.170.3421.071100
2.21-2.2640.30626040.8820.1750.3531.19100
2.26-2.3240.23626120.9320.1350.2731.069100
2.32-2.3940.21926180.940.1250.2531.058100
2.39-2.4740.20326040.9460.1160.2351.031100
2.47-2.5640.17826170.9560.1010.2051.055100
2.56-2.6640.15426350.9640.0870.1771.021100
2.66-2.7840.13526160.9740.0760.1551.054100
2.78-2.9340.11726440.9780.0670.1351.032100
2.93-3.1140.10326370.9810.0590.1191.052100
3.11-3.3540.08926350.9840.0510.1031.091100
3.35-3.6940.07726790.990.0440.0891.039100
3.69-4.2240.06526840.9920.0370.0751.066100
4.22-5.323.90.05627070.9940.0320.0651.003100
5.32-503.70.0527930.9950.0290.058197.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000v705data scaling
PDB_EXTRACT3.22data extraction
REFMAC5.8.0158phasing
HKLdata scaling
HKL-2000v705data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4KU3

4ku3


Resolution: 1.968→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.774 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 2646 5 %RANDOM
Rwork0.1688 ---
obs0.1711 49981 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.39 Å2 / Biso mean: 33.923 Å2 / Biso min: 7.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2--0.6 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: final / Resolution: 1.968→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5197 0 12 178 5387
Biso mean--53.54 33.91 -
Num. residues----685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0195336
X-RAY DIFFRACTIONr_bond_other_d0.0020.025123
X-RAY DIFFRACTIONr_angle_refined_deg2.411.9647233
X-RAY DIFFRACTIONr_angle_other_deg1.225311842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0835695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64524.091220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96815930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0411539
X-RAY DIFFRACTIONr_chiral_restr0.1510.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025979
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021040
LS refinement shellResolution: 1.968→2.019 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 198 -
Rwork0.234 3461 -
all-3659 -
obs--95.36 %
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)
10.3033-0.08660.07710.17670.06610.1261-0.0312-0.0104-0.01180.03880.02770.03590.04440.00970.00350.03690.00130.010.00650.00030.0279-10.68157.1534-2.2047
20.07260.0606-0.1530.2367-0.16360.3655-0.01520.00150.0098-0.09180.012-0.01580.0512-0.02590.00310.072-0.01070.00660.013-0.01150.0143-13.569223.8681-27.4817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 358
2X-RAY DIFFRACTION2B19 - 358

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