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- PDB-3s20: Crystal structure of cerulenin bound Xanthomonas campestri OleA (soak) -

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Basic information

Entry
Database: PDB / ID: 3s20
TitleCrystal structure of cerulenin bound Xanthomonas campestri OleA (soak)
Components3-oxoacyl-[ACP] synthase III
KeywordsTRANSFERASE / Non-decarboxylative Claisen Condensation Reaction
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
Chem-CER / DI(HYDROXYETHYL)ETHER / Acyl-CoA:acyl-CoA alkyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8796 Å
AuthorsGoblirsch, B.R. / Wilmot, C.M.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal Structures of Xanthomonas campestris OleA Reveal Features That Promote Head-to-Head Condensation of Two Long-Chain Fatty Acids.
Authors: Goblirsch, B.R. / Frias, J.A. / Wackett, L.P. / Wilmot, C.M.
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Sep 13, 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)75,2766
Polymers74,6142
Non-polymers6634
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-2 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.653, 85.358, 103.020
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: 37306.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: fabH, XCC0212 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PDX2
#2: Chemical ChemComp-CER / (2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE / CERULENIN / Cerulenin


Mass: 225.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19NO3 / Comment: antifungal, antibiotic*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 18% 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-B / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2011
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: 1.8796→50 Å / Num. all: 59154 / Num. obs: 59154 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 40.7
Reflection shellResolution: 1.8796→1.91 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3ROW

3row


Resolution: 1.8796→30.487 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 18.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 2923 5.03 %Copy free R from PDB ENTRY 3ROW
Rwork0.1691 ---
all0.1706 58105 --
obs0.1706 58105 98.07 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.547 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5844 Å2-0 Å20 Å2
2---3.0531 Å20 Å2
3---1.4687 Å2
Refinement stepCycle: LAST / Resolution: 1.8796→30.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5087 0 46 467 5600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085472
X-RAY DIFFRACTIONf_angle_d1.0357462
X-RAY DIFFRACTIONf_dihedral_angle_d13.9712095
X-RAY DIFFRACTIONf_chiral_restr0.072882
X-RAY DIFFRACTIONf_plane_restr0.004969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8796-1.91040.24571240.20382416X-RAY DIFFRACTION91
1.9104-1.94330.23251390.18242458X-RAY DIFFRACTION94
1.9433-1.97870.19471280.16652527X-RAY DIFFRACTION96
1.9787-2.01670.24361350.16482533X-RAY DIFFRACTION96
2.0167-2.05790.23111400.16672559X-RAY DIFFRACTION96
2.0579-2.10260.22641460.17072554X-RAY DIFFRACTION97
2.1026-2.15150.21541320.17042629X-RAY DIFFRACTION98
2.1515-2.20530.23421350.15712586X-RAY DIFFRACTION98
2.2053-2.26490.22181370.16112636X-RAY DIFFRACTION99
2.2649-2.33150.2311390.16142611X-RAY DIFFRACTION99
2.3315-2.40680.18541410.16342630X-RAY DIFFRACTION99
2.4068-2.49270.21721440.172631X-RAY DIFFRACTION99
2.4927-2.59250.23111360.16522650X-RAY DIFFRACTION99
2.5925-2.71040.20561430.17032680X-RAY DIFFRACTION100
2.7104-2.85320.21281470.17862663X-RAY DIFFRACTION100
2.8532-3.03180.2421430.18372678X-RAY DIFFRACTION100
3.0318-3.26570.20441390.18582704X-RAY DIFFRACTION100
3.2657-3.59380.18291400.17552689X-RAY DIFFRACTION100
3.5938-4.11280.17381450.15622730X-RAY DIFFRACTION100
4.1128-5.17760.14511420.14112754X-RAY DIFFRACTION100
5.1776-30.49130.191480.18862864X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.1328 Å / Origin y: 15.2037 Å / Origin z: -14.4082 Å
111213212223313233
T0.069 Å2-0.0041 Å2-0.0035 Å2-0.088 Å2-0.0085 Å2--0.0792 Å2
L0.2009 °2-0.1558 °2-0.0416 °2-0.6268 °2-0.0346 °2--0.2794 °2
S0.0261 Å °0.0245 Å °-0.0362 Å °-0.0826 Å °-0.0204 Å °0.0648 Å °0.0292 Å °0.0006 Å °0.002 Å °
Refinement TLS groupSelection details: (chain 'A') or (chain 'B')

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