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- PDB-6b2r: Crystal structure of Xanthomonas campestris OleA H285A -

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Basic information

Entry
Database: PDB / ID: 6b2r
TitleCrystal structure of Xanthomonas campestris OleA H285A
Components(3-oxoacyl-[ACP] synthase III) x 2
KeywordsTRANSFERASE / Thiolase / OleA / 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: 1.77 Å
AuthorsJensen, M.R. / Goblirsch, B.R. / Esler, M.A. / Christenson, J.K. / Mohamed, F.A. / Wackett, L.P. / Wilmot, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008700 United States
BioTechnology Institute1000014885 10866 MNT11 United States
CitationJournal: FEBS Lett. / Year: 2018
Title: The role of OleA His285 in orchestration of long-chain acyl-coenzyme A substrates.
Authors: Jensen, M.R. / Goblirsch, B.R. / Esler, M.A. / Christenson, J.K. / Mohamed, F.A. / Wackett, L.P. / Wilmot, C.M.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)77,7514
Polymers77,5672
Non-polymers1842
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-14 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.176, 85.609, 103.000
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: 38775.379 Da / Num. of mol.: 1 / Mutation: H285A
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 (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8PDX2, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Protein 3-oxoacyl-[ACP] synthase III


Mass: 38791.379 Da / Num. of mol.: 1 / Mutation: H285A
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 (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8PDX2, beta-ketoacyl-[acyl-carrier-protein] synthase I
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.43 % / Mosaicity: 0.696 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 18% PEG 8000, 110 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 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02235 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 71384 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.038 / Rrim(I) all: 0.102 / Χ2: 0.983 / Net I/σ(I): 15.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.85.60.87734830.690.4060.971.08598.1
1.8-1.835.80.76935190.7740.3460.8451.11799.4
1.83-1.876.30.66735080.8350.2880.7281.07299.8
1.87-1.916.60.73835410.7340.3120.8031.1699.8
1.91-1.956.60.56135480.7870.2360.611.38599.9
1.95-1.996.80.36735180.9340.1510.3970.94999.9
1.99-2.046.90.31335310.9530.1290.3390.982100
2.04-2.16.70.35235530.8390.1480.3821.03699.9
2.1-2.166.90.20535570.9790.0840.2221.093100
2.16-2.236.90.18235340.9840.0740.1961.00799.9
2.23-2.316.80.25735660.8750.1080.2790.81799.9
2.31-2.47.10.13235540.990.0530.1431.039100
2.4-2.517.20.11235500.9920.0450.1211.079100
2.51-2.647.30.09835910.9940.0390.1051.052100
2.64-2.817.30.09335710.9940.0370.10.658100
2.81-3.037.40.07135940.9970.0280.0761.034100
3.03-3.337.40.05736110.9980.0230.0621.015100
3.33-3.817.30.05436240.9980.0220.0590.55599.9
3.81-4.87.10.04236620.9990.0170.0450.69699.7
4.8-506.70.03837690.9980.0160.0410.97197.9

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Processing

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

3row


Resolution: 1.77→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.111 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 3568 5 %RANDOM
Rwork0.1749 ---
obs0.1766 67663 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.7 Å2 / Biso mean: 26.207 Å2 / Biso min: 9.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0 Å2
2---0.73 Å20 Å2
3---0.24 Å2
Refinement stepCycle: final / Resolution: 1.77→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5182 0 12 261 5455
Biso mean--34.47 28.58 -
Num. residues----683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0195373
X-RAY DIFFRACTIONr_bond_other_d0.0020.025154
X-RAY DIFFRACTIONr_angle_refined_deg2.3731.9667292
X-RAY DIFFRACTIONr_angle_other_deg1.167311921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79324.118221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06115936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6851539
X-RAY DIFFRACTIONr_chiral_restr0.1480.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026047
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021052
LS refinement shellResolution: 1.769→1.814 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 263 -
Rwork0.208 4811 -
all-5074 -
obs--96.85 %
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)
10.1811-0.04430.04770.15140.04450.0531-0.0157-0.0032-0.01660.03730.00760.02530.02230.00730.00810.0289-0.00120.00720.03890.00390.0106-10.83977.0197-2.4414
20.03050.0213-0.08670.1993-0.05880.2766-0.0013-0.0046-0.0012-0.0597-0.0046-0.0080.0175-0.01660.00590.04820.00240.00270.0394-0.00240.0005-13.416923.7709-27.2327
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 358
2X-RAY DIFFRACTION2B20 - 358

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