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- PDB-3led: Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase II... -

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Basic information

Entry
Database: PDB / ID: 3led
TitleCrystal structure of 3-oxoacyl-(acyl carrier protein) synthase III from Rhodopseudomonas palustris CGA009
Components3-oxoacyl-acyl carrier protein synthase III
KeywordsTRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Acyltransferase
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
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
FORMIC ACID / 3-oxoacyl-acyl carrier protein synthase III
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsChang, C. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase III from Rhodopseudomonas palustris CGA009
Authors: Chang, C. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJan 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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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 III
B: 3-oxoacyl-acyl carrier protein synthase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5524
Polymers86,4602
Non-polymers922
Water23,3831298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.997, 114.790, 60.429
Angle α, β, γ (deg.)90.00, 96.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 3-oxoacyl-acyl carrier protein synthase III


Mass: 43230.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA1298 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative
References: UniProt: Q6NA87, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1298 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Sodium Formate, 20%PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2009
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 133666 / Num. obs: 133399 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 40.4
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 4.62 / Num. unique all: 6522 / % possible all: 97

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.895 / SU ML: 0.034 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.06
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16843 6711 5 %RANDOM
Rwork0.14473 ---
all0.14593 133182 --
obs0.14593 126471 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.341 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å2-0.18 Å2
2--0.57 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5721 0 6 1298 7025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226254
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9488517
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8785838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18923.967305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.477151066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0881556
X-RAY DIFFRACTIONr_chiral_restr0.10.2919
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214947
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7531.53953
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31926382
X-RAY DIFFRACTIONr_scbond_it2.33432301
X-RAY DIFFRACTIONr_scangle_it3.7234.52119
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 469 -
Rwork0.205 9148 -
obs-9617 97.27 %
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)
10.6240.2550.12380.3754-0.01160.2269-0.0104-0.05340.1263-0.04830.0120.0899-0.0404-0.0484-0.00160.01980.0027-0.00460.01550.00030.03923.671530.196412.2162
21.7316-0.26280.1140.0427-0.03020.2197-0.03450.0290.00020.00320.00650.00410.04410.04670.0280.02960.00070.00910.02840.0020.034458.973731.845813.9031
30.14940.10880.03620.1903-0.02140.1110.0024-0.00250.0269-0.00540.01380.0272-0.0109-0.0159-0.01620.0126-0.00470.00350.0158-0.00050.027327.280122.789416.4888
40.02240.0402-0.00660.09840.09130.48170.0002-0.0014-0.0093-0.01160.012-0.016800.0354-0.01220.0234-0.00860.00350.0296-0.00240.026446.308612.364320.6966
50.44080.0353-0.01020.1388-0.14860.2141-0.01490.03880.031-0.03040.03630.0181-0.0001-0.0139-0.02140.0323-0.0169-0.00780.0280.00280.012827.80925.3564-2.9786
60.19930.20050.20610.33950.10420.3340.02710.015-0.0497-0.04290.0328-0.00520.10380.0164-0.05990.0549-0.0084-0.01770.02740.01210.042227.4501-8.656820.9193
70.39610.52360.60670.72120.76041.03590.0231-0.0264-0.02550.00350.0281-0.03120.0024-0.1206-0.05110.0202-0.01320.01120.08980.00970.011742.5772.557749.7484
80.22940.02160.05130.1213-0.06790.10010.0037-0.013-0.0254-0.02540.01310.00940.0265-0.0006-0.01680.0214-0.0153-0.0030.02110.00290.017829.6321-0.482419.684
90.49860.3086-0.17380.6066-0.22490.1460.0343-0.0475-0.00590.0352-0.0317-0.0285-0.0262-0.0059-0.00260.0326-0.01440.00880.0241-0.00090.018837.716816.210133.1786
100.22330.2532-0.0840.42180.02590.1585-0.0168-0.02070.0165-0.00290.00920.05960.00860.04640.00760.0201-0.01150.00320.02610.01050.043613.684-5.922229.844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION2A21 - 57
3X-RAY DIFFRACTION3A58 - 234
4X-RAY DIFFRACTION4A235 - 259
5X-RAY DIFFRACTION5A260 - 371
6X-RAY DIFFRACTION6B1 - 20
7X-RAY DIFFRACTION7B21 - 57
8X-RAY DIFFRACTION8B58 - 234
9X-RAY DIFFRACTION9B235 - 259
10X-RAY DIFFRACTION10B260 - 371

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