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- PDB-4ktm: Crystal Structure of C143S Xanthomonas campestris OleA -

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Basic information

Entry
Database: PDB / ID: 4ktm
TitleCrystal Structure of C143S Xanthomonas campestris OleA
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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Acyl-CoA:acyl-CoA alkyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.36 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 20, 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)74,2807
Polymers73,7612
Non-polymers5195
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-8 kcal/mol
Surface area24790 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
DetailsThe asymmetric unit of the structure corresponds to the biological assembly.

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Components

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


Mass: 36880.250 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.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#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.: 341 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
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 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 10, 2012
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. all: 211791 / Num. obs: 211791 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 7
Reflection shellResolution: 2.36→2.4 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 3.1 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3ROW

3row


Resolution: 2.36→32.828 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 1497 4.99 %R-free selection based on R-free set from WT OleA data (3ROW)
Rwork0.1657 ---
obs0.1683 30020 98.8 %-
all-30020 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.36→32.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5152 0 33 341 5526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035414
X-RAY DIFFRACTIONf_angle_d0.7557353
X-RAY DIFFRACTIONf_dihedral_angle_d11.9332011
X-RAY DIFFRACTIONf_chiral_restr0.052860
X-RAY DIFFRACTIONf_plane_restr0.003956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3601-2.43630.26261130.18472269X-RAY DIFFRACTION87
2.4363-2.52330.27311290.18052585X-RAY DIFFRACTION100
2.5233-2.62430.25291420.18042569X-RAY DIFFRACTION100
2.6243-2.74370.28121370.18972591X-RAY DIFFRACTION100
2.7437-2.88820.32051430.20432575X-RAY DIFFRACTION100
2.8882-3.06910.26851360.20052605X-RAY DIFFRACTION100
3.0691-3.30580.23391330.18132624X-RAY DIFFRACTION100
3.3058-3.63810.18791430.16022608X-RAY DIFFRACTION100
3.6381-4.16370.20131390.14142629X-RAY DIFFRACTION100
4.1637-5.24230.18631370.13212676X-RAY DIFFRACTION100
5.2423-32.8310.16521450.16442792X-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)
11.1192-0.33150.07551.6850.08330.4358-0.0215-0.0868-0.04920.108-0.02190.13560.0179-0.02740.03660.1571-0.01620.01820.1785-0.00380.143-10.35876.7879-2.632
20.91320.0875-0.37871.36920.58532.29580.09760.1365-0.0803-0.4546-0.11330.1817-0.1273-0.15550.0210.29860.0374-0.05370.18750.01410.2177-12.692223.7481-27.3062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 19:358)
2X-RAY DIFFRACTION2(chain B and resid 21:358)

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