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- PDB-4dfe: Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase II... -

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Basic information

Entry
Database: PDB / ID: 4dfe
TitleCrystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia xenovorans
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTRANSFERASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 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
Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionJan 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3
C: 3-oxoacyl-[acyl-carrier-protein] synthase 3
D: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,3545
Polymers141,2924
Non-polymers621
Water5,224290
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
D: 3-oxoacyl-[acyl-carrier-protein] synthase 3


Theoretical massNumber of molelcules
Total (without water)70,6462
Polymers70,6462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-25 kcal/mol
Surface area20610 Å2
MethodPISA
2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3
C: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7083
Polymers70,6462
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-24 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.990, 67.030, 89.200
Angle α, β, γ (deg.)113.720, 89.980, 100.250
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-oxoacyl-[acyl-carrier-protein] synthase III / Beta-ketoacyl-ACP synthase III


Mass: 35322.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: fabH, Bxeno_A3336, Bxe_A1072 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13VL5, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Internal tracking number 228627G11. Crystallant (Wizard III/IV G11): 20% PEG 6000, 0.1 M Hepes pH 7.0, 200 mM NaCl. Protein: BuxeA.00171.c.A1 PW33645 at 35 mg/ml in a buffer consisting of 25 ...Details: Internal tracking number 228627G11. Crystallant (Wizard III/IV G11): 20% PEG 6000, 0.1 M Hepes pH 7.0, 200 mM NaCl. Protein: BuxeA.00171.c.A1 PW33645 at 35 mg/ml in a buffer consisting of 25 mM HEPES pH 7.0, 300-500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol. Cryoprotection was achieved by supplementing the reservoir solution with 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2011
RadiationMonochromator: Asymmetric curved crystal, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 49242 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 36.372 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.35-2.413.30.5022.511990364597.5
2.41-2.480.4492.811593352797.3
2.48-2.550.3653.411167339097.3
2.55-2.630.2954.110980334997.5
2.63-2.710.2714.610687325997.4
2.71-2.810.2195.610304314197.6
2.81-2.910.1876.69954303897.6
2.91-3.030.14989534291598
3.03-3.170.1149.99096278497.8
3.17-3.320.09312.28777268897.8
3.32-3.50.07614.58278253597.5
3.5-3.720.0617.57822240397.9
3.72-3.970.04721.57414228498.5
3.97-4.290.03924.56806210498.4
4.29-4.70.03527.26338196398.3
4.7-5.250.03725.95641176998.7
5.25-6.070.04123.44873155598.5
6.07-7.430.03625.74394132298.7
7.43-10.510.02634.43348101399.4
10.51-500.02539.8183055897.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.46 Å
Translation2.5 Å48.46 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: molecular replacement, molecular replacement
Starting model: PDB entry 1HN9

1hn9


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.888 / SU B: 18.849 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2488 5.1 %RANDOM
Rwork0.227 ---
obs0.229 49242 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.633 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0.43 Å2-1.09 Å2
2---0.37 Å21.88 Å2
3---1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9403 0 4 290 9697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199591
X-RAY DIFFRACTIONr_bond_other_d0.0060.026140
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.94613070
X-RAY DIFFRACTIONr_angle_other_deg1.167314967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06951287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69623.403382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.564151406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8361569
X-RAY DIFFRACTIONr_chiral_restr0.0790.21563
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211012
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021981
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 188 -
Rwork0.298 3446 -
all-3634 -
obs--97.45 %
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)
10.2854-0.85630.34222.9563-0.34191.89150.1467-0.0233-0.03990.02720.1346-0.06730.85860.1989-0.28130.42740.0681-0.14870.1930.02760.198633.0782-14.860610.4206
21.0585-0.46550.27482.5316-0.58631.162-0.00990.1059-0.00440.10480.0226-0.25430.19440.089-0.01270.13960.0102-0.04380.1324-0.01750.138427.8987-3.632-0.1938
30.1687-0.363-0.26092.4042-0.35271.3093-0.07740.00020.01660.74670.0807-0.2960.10710.0343-0.00340.41240.0468-0.18110.1013-0.01670.13227.8655-2.578415.815
42.3729-0.9925-1.08351.8606-0.2462.28520.0894-0.4122-0.30510.35920.01180.34880.3429-0.0034-0.10120.3769-0.14110.01390.15810.05860.125713.5166-13.524416.7055
50.9468-0.47960.47872.4332-0.38631.71130.0498-0.0724-0.17940.37440.04190.0840.4838-0.0761-0.09170.3056-0.0418-0.00960.10650.03780.143119.0625-15.0449.6381
62.0432-1.51261.19367.62420.90111.19040.32020.2162-0.6613-0.13470.2454-0.25060.21150.2119-0.56560.20550.0197-0.07260.247-0.00880.361215.2088-42.4779-35.8975
70.9949-0.15520.2352.0178-0.17650.63710.04520.08910.0857-0.42450.0650.10680.1215-0.0056-0.11030.2187-0.0141-0.04540.13360.00540.09595.5743-29.641-41.5889
81.22840.07920.35372.041-0.04290.33110.1025-0.131-0.06730.01360.0129-0.22020.04230.0096-0.11540.0946-0.0068-0.02810.13510.00390.133315.3405-29.5498-28.7329
91.0198-0.4479-0.33662.991-0.62840.8452-0.0513-0.1764-0.1184-0.02530.1840.36980.07080.0208-0.13270.1107-0.003-0.00670.19530.03710.1831.7422-37.6579-19.8303
101.1225-0.28910.96861.5719-0.26021.52420.09060.0348-0.0779-0.12850.13090.27690.1902-0.0541-0.22140.1318-0.0249-0.03250.09830.01850.20261.5518-39.9872-28.2468
112.29641.2353-1.93393.0742-1.16313.83570.1838-0.09190.0992-0.2351-0.0705-0.1999-0.7390.2371-0.11330.2873-0.0442-0.01940.0192-0.00190.134315.86211.4705-42.1392
120.30890.1682-0.17833.1739-0.53181.1808-0.1456-0.0680.0261-0.04870.0351-0.1301-0.1794-0.00050.11050.14410.0115-0.01660.1564-0.0020.159510.8853-10.1117-30.922
130.25870.64560.10272.4983-0.71721.7107-0.16260.03010.0469-0.75590.1663-0.0049-0.0355-0.0019-0.00370.394-0.03460.07210.1015-0.00690.116810.6713-10.9901-46.8832
143.94231.66771.28321.64760.85380.7573-0.16230.59730.2758-0.41840.11110.4683-0.2131-0.00270.05120.26960.0466-0.12930.20840.08820.2494-3.33940.1252-47.3916
150.85330.0456-0.75953.11990.15531.2163-0.03340.07740.1947-0.41150.04310.3054-0.2723-0.0938-0.00960.2930.0405-0.11350.10180.03570.23531.90131.5307-40.5194
167.2272.7084-0.37572.70210.09661.60810.1873-0.20940.39760.25920.0788-0.0214-0.26040.1574-0.26610.12770.01230.05980.0406-0.02720.169131.001928.91974.3311
170.86290.0306-0.06461.2672-0.04830.89770.0879-0.0231-0.03820.43620.0538-0.1056-0.0268-0.008-0.14160.189-0.00280.00940.1249-0.00550.135822.600815.895710.5599
180.59150.4253-0.35981.7124-0.1680.48960.1540.07360.1036-0.03090.0032-0.2718-0.01520.0659-0.15720.09520.02450.05570.1797-0.03630.170731.692315.855-2.6393
193.74921.6609-0.69282.1243-0.19411.74280.06140.36650.1027-0.0050.0741-0.0044-0.03820.0927-0.13550.07420.0060.03030.16270.06840.181818.925424.0422-12.1456
201.05850.1944-0.40041.6209-0.661.81490.133-0.09570.06260.1830.12860.1462-0.1737-0.1022-0.26160.10560.0140.09250.12950.03190.184718.558326.2575-2.9724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 45
2X-RAY DIFFRACTION2A46 - 157
3X-RAY DIFFRACTION3A158 - 232
4X-RAY DIFFRACTION4A233 - 269
5X-RAY DIFFRACTION5A270 - 329
6X-RAY DIFFRACTION6B5 - 45
7X-RAY DIFFRACTION7B46 - 157
8X-RAY DIFFRACTION8B158 - 232
9X-RAY DIFFRACTION9B233 - 269
10X-RAY DIFFRACTION10B270 - 329
11X-RAY DIFFRACTION11C5 - 45
12X-RAY DIFFRACTION12C46 - 157
13X-RAY DIFFRACTION13C158 - 232
14X-RAY DIFFRACTION14C233 - 269
15X-RAY DIFFRACTION15C270 - 329
16X-RAY DIFFRACTION16D5 - 45
17X-RAY DIFFRACTION17D46 - 157
18X-RAY DIFFRACTION18D158 - 232
19X-RAY DIFFRACTION19D233 - 269
20X-RAY DIFFRACTION20D270 - 329

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