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- PDB-1o6u: The Crystal Structure of Human Supernatant Protein Factor -

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Basic information

Entry
Database: PDB / ID: 1o6u
TitleThe Crystal Structure of Human Supernatant Protein Factor
ComponentsSEC14-LIKE PROTEIN 2
KeywordsTRANSFERASE / LIPID TRANSFER / CRAL_TRIO / LIPID BINDING
Function / homology
Function and homology information


vitamin E binding / regulation of cholesterol biosynthetic process / phospholipid binding / positive regulation of DNA-templated transcription / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
GOLD domain / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / GOLD domain superfamily / GOLD domain / GOLD domain profile. / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily ...GOLD domain / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / GOLD domain superfamily / GOLD domain / GOLD domain profile. / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Jelly Rolls / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / SEC14-like protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.05 Å
AuthorsStocker, A. / Schulze-Briese, C. / Tomizaki, T.
CitationJournal: Structure / Year: 2002
Title: Crystal Structure of Human Supernatant Protein Factor
Authors: Stocker, A. / Tomizaki, T. / Schulze-Briese, C. / Baumann, U.
History
DepositionOct 16, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 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: SEC14-LIKE PROTEIN 2
C: SEC14-LIKE PROTEIN 2
E: SEC14-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,9416
Polymers140,1723
Non-polymers7693
Water11,656647
1
A: SEC14-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9802
Polymers46,7241
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: SEC14-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9802
Polymers46,7241
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: SEC14-LIKE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9802
Polymers46,7241
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.794, 84.240, 87.111
Angle α, β, γ (deg.)116.26, 102.39, 99.87
Int Tables number1
Space group name H-MP1

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Components

#1: Protein SEC14-LIKE PROTEIN 2 / SUPERNATANT PROTEIN FACTOR


Mass: 46723.992 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O76054
#2: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 647 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCARRIER PROTEIN THAT BINDS TO SOME HYDROPHOBIC MOLECULES AND PROMOTES THEIR TRANSFER BETWEEN THE ...CARRIER PROTEIN THAT BINDS TO SOME HYDROPHOBIC MOLECULES AND PROMOTES THEIR TRANSFER BETWEEN THE DIFFERENT CELLULAR SITES. BINDS WITH HIGH AFFINITY TO ALPHA-TOCOPHEROL. ALSO BINDS WITH A WEAKER AFFINITY TO OTHER TOCOPHEROLS AND TO TOCOTRIENOLS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growpH: 8.3 / Details: pH 8.30
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 %(w/v)PEG33501reservoir
25 %(w/v)glycerol1reservoir
3200 mMsodium citrate1reservoirpH8.3
42 mMEDTA1drop
52 mMdithiothreitol1drop
640 mM1dropNaCl
720 mMTris-HCl1droppH7.4
820 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97884
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97884 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 184572 / % possible obs: 97.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 15.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.9 / % possible all: 97.1
Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 20 Å / Num. measured all: 715326 / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 97.1 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.05→27.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1540738.85 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINEMENT CARIIED OUT AGAINST PEAK ANOMALOUS DATA. SCATTERING FACTORS REFINED IN CNS: FP =-8.003; FDP=4.56
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2754 1.6 %RANDOM
Rwork0.204 ---
obs0.204 175712 98.7 %-
Solvent computationSolvent model: MASK / Bsol: 39.1085 Å2 / ksol: 0.367266 e/Å3
Displacement parametersBiso mean: 26.35 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å21.67 Å20.19 Å2
2---0.03 Å20.84 Å2
3----3.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.05→27.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9502 0 54 647 10203
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it3.32
X-RAY DIFFRACTIONc_scangle_it52.5
LS refinement shellResolution: 2.05→2.14 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 355 1.7 %
Rwork0.269 20739 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3PLM_XPLOR_PAR.TXTPLM_XPLOR_PAR.TXT
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 175152 / Num. reflection Rfree: 2836 / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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