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- PDB-3ont: The Crystal Structure of Spot14, a modulator of lipogenesis -

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Basic information

Entry
Database: PDB / ID: 3ont
TitleThe Crystal Structure of Spot14, a modulator of lipogenesis
ComponentsSpot 14 protein
KeywordsUNKNOWN FUNCTION / alpha-helical / helical bundle
Function / homology
Function and homology information


Carnitine metabolism / regulation of triglyceride biosynthetic process / regulation of lipid biosynthetic process / response to bacterium / lipid metabolic process / protein homodimerization activity / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Helix Hairpins - #1610 / Spot 14 family / Thyroid hormone-inducible hepatic protein Spot 14 / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Thyroid hormone-inducible hepatic protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsColbert, C.L. / Kwon, H.J. / Deisenhofer, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure of Spot 14, a modulator of fatty acid synthesis.
Authors: Colbert, C.L. / Kim, C.W. / Moon, Y.A. / Henry, L. / Palnitkar, M. / McKean, W.B. / Fitzgerald, K. / Deisenhofer, J. / Horton, J.D. / Kwon, H.J.
History
DepositionAug 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spot 14 protein


Theoretical massNumber of molelcules
Total (without water)17,5391
Polymers17,5391
Non-polymers00
Water1086
1
A: Spot 14 protein

A: Spot 14 protein


Theoretical massNumber of molelcules
Total (without water)35,0782
Polymers35,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation43_555-x+1/2,-z+1/2,-y+1/21
Buried area5290 Å2
ΔGint-59 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.951, 144.951, 144.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Spot 14 protein / Thyroid hormone-inducible hepatic protein / SPOT14 / S14


Mass: 17538.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: S14, spot14, Thrsp / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62264
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.62 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.100 M MES pH 6.0, 0.015 M magnesium chloride, 5% (w/v) polyethylene glycol 3000 and 30% (v/v) polyethylene glycol 200, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2009
RadiationMonochromator: sagittally focused Si 111 + sagittally focused Si 220
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. all: 7941 / Num. obs: 7919 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 92.2 Å2 / Rsym value: 0.063 / Net I/σ(I): 14.9
Reflection shellResolution: 2.64→2.69 Å / Redundancy: 7.5 % / Num. unique all: 379 / Rsym value: 0.552 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.65→38.74 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.915 / SU B: 18.171 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24912 363 4.6 %RANDOM
Rwork0.22305 ---
all0.22424 7894 --
obs0.22424 7512 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.221 Å2
Refinement stepCycle: LAST / Resolution: 2.65→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 0 0 6 908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022918
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9711241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.735109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43623.95343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.52215166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.24156
X-RAY DIFFRACTIONr_chiral_restr0.1140.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021675
X-RAY DIFFRACTIONr_mcbond_it1.462558
X-RAY DIFFRACTIONr_mcangle_it2.7013908
X-RAY DIFFRACTIONr_scbond_it1.8373360
X-RAY DIFFRACTIONr_scangle_it2.5873333
LS refinement shellResolution: 2.648→2.717 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 36 -
Rwork0.33 528 -
obs--99.65 %
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)
19.0733-0.34552.61421.39860.28720.9037-0.160.07030.0871-0.09650.11940.3711-0.04680.11620.04070.2213-0.0223-0.04180.33460.08320.356550.806718.787768.7064
211.28832.0084.96320.40630.74332.59210.24850.216-0.3779-0.03030.0277-0.0070.30690.211-0.27610.2405-0.0129-0.03660.37090.07050.341453.72919.775368.6068
312.3312.85728.20351.02871.7945.6180.29590.6148-0.25880.0721-0.0912-0.09880.36880.4459-0.20470.222-0.01670.00060.37860.08580.332331.61410.988360.8276
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 45
2X-RAY DIFFRACTION2A49 - 76
3X-RAY DIFFRACTION3A105 - 149

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