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- PDB-4tlg: Crystal structure of SEC14-like protein 4 (SEC14L4) -

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Basic information

Entry
Database: PDB / ID: 4tlg
TitleCrystal structure of SEC14-like protein 4 (SEC14L4)
ComponentsSEC14-like protein 4
KeywordsTRANSPORT PROTEIN / SEC14L4
Function / homology
Function and homology information


lipid binding / 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 ...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
UNDECANOIC ACID / SEC14-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsVollmar, M. / Kopec, J. / Kiyani, W. / Shrestha, L. / Sorrell, F. / Krojer, T. / Williams, E. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. ...Vollmar, M. / Kopec, J. / Kiyani, W. / Shrestha, L. / Sorrell, F. / Krojer, T. / Williams, E. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.
CitationJournal: To Be Published
Title: Crystal structure of SEC14-like protein 4 (SEC14L4)
Authors: Vollmar, M.
History
DepositionMay 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SEC14-like protein 4
B: SEC14-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,93130
Polymers92,9452
Non-polymers1,98628
Water8,305461
1
A: SEC14-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,71419
Polymers46,4721
Non-polymers1,24118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SEC14-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,21711
Polymers46,4721
Non-polymers74510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.185, 79.495, 82.395
Angle α, β, γ (deg.)90.00, 95.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SEC14-like protein 4 / Tocopherol-associated protein 3


Mass: 46472.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC14L4, TAP3 / Plasmid: pNIC28Bsa / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9UDX3
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-11A / UNDECANOIC ACID


Mass: 186.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22O2 / Comment: antifungal*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Magnesium Chloride -- 0.1M tris pH 8.5 -- 25%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.77→37.33 Å / Num. obs: 640884 / % possible obs: 95.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.2

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Processing

SoftwareName: REFMAC / Version: 5.8.0071 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OLM

1olm


Resolution: 1.77→37.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.344 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19425 4425 5 %RANDOM
Rwork0.13843 ---
obs0.14118 83615 95.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.583 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0 Å2-0.22 Å2
2---0.08 Å2-0 Å2
3---0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.77→37.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6182 0 130 461 6773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196514
X-RAY DIFFRACTIONr_bond_other_d0.0010.026238
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9838778
X-RAY DIFFRACTIONr_angle_other_deg0.803314350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5495808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93524.415299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.619151123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0191539
X-RAY DIFFRACTIONr_chiral_restr0.0830.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021465
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_it3.6832.5313163
X-RAY DIFFRACTIONr_mcbond_other3.6822.5293162
X-RAY DIFFRACTIONr_mcangle_it4.4573.8033955
X-RAY DIFFRACTIONr_mcangle_other4.4573.8043956
X-RAY DIFFRACTIONr_scbond_it4.332.9023351
X-RAY DIFFRACTIONr_scbond_other4.332.9023352
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2094.1944811
X-RAY DIFFRACTIONr_long_range_B_refined5.70420.927358
X-RAY DIFFRACTIONr_long_range_B_other5.70420.9227359
X-RAY DIFFRACTIONr_rigid_bond_restr2.411312752
X-RAY DIFFRACTIONr_sphericity_free33.5315219
X-RAY DIFFRACTIONr_sphericity_bonded16.857512874
LS refinement shellResolution: 1.774→1.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 320 -
Rwork0.148 6166 -
obs-32318 95.76 %

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