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- PDB-5yqp: Crystal structure of the second StARkin domain of Lam4 -

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Basic information

Entry
Database: PDB / ID: 5yqp
TitleCrystal structure of the second StARkin domain of Lam4
ComponentsMembrane-anchored lipid-binding protein LAM4
KeywordsTRANSPORT PROTEIN / ligand binding domain / sterol / lipid transport / LTC3 / Lam4 / StARkin
Function / homology
Function and homology information


intracellular sterol transport / endoplasmic reticulum-plasma membrane contact site / sterol transfer activity / sterol binding / sterol transport / cortical endoplasmic reticulum / endoplasmic reticulum membrane / mitochondrion / plasma membrane
Similarity search - Function
VASt domain / VAD1 Analog of StAR-related lipid transfer domain / VASt domain profile. / : / domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins / GRAM domain / GRAM domain / PH-like domain superfamily
Similarity search - Domain/homology
Membrane-anchored lipid-binding protein LAM4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTong, J. / Manik, K.M. / IM, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF-2017R1A2B4004914 Korea, Republic Of
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis of sterol recognition and nonvesicular transport by lipid transfer proteins anchored at membrane contact sites
Authors: Tong, J. / Manik, M.K. / Im, Y.J.
History
DepositionNov 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Membrane-anchored lipid-binding protein LAM4
B: Membrane-anchored lipid-binding protein LAM4


Theoretical massNumber of molelcules
Total (without water)42,5902
Polymers42,5902
Non-polymers00
Water6,341352
1
A: Membrane-anchored lipid-binding protein LAM4


Theoretical massNumber of molelcules
Total (without water)21,2951
Polymers21,2951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Membrane-anchored lipid-binding protein LAM4


Theoretical massNumber of molelcules
Total (without water)21,2951
Polymers21,2951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.337, 89.074, 111.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1241-

HOH

21A-1253-

HOH

31A-1336-

HOH

41A-1387-

HOH

51B-1294-

HOH

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Components

#1: Protein Membrane-anchored lipid-binding protein LAM4 / Lipid transfer at contact site protein 3 / Lipid transfer protein anchored at membrane contact sites 1


Mass: 21295.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: LAM4, LTC3, YHR080C / Plasmid: pHIS2-Thr
Details (production host): An N-terminal hexa-histidine tag fusion
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38800
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1M Bicine-NaOH pH 9.0, 30% PEG1500, 0.1M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 37918 / % possible obs: 99.6 % / Redundancy: 8.8 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 51.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 8.2 / Num. unique obs: 1880 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YQJ

5yqj


Resolution: 1.7→27.232 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.05
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 1895 5 %Random selection
Rwork0.2022 ---
obs0.2043 37910 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→27.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 0 352 3272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072974
X-RAY DIFFRACTIONf_angle_d0.9234030
X-RAY DIFFRACTIONf_dihedral_angle_d16.3041822
X-RAY DIFFRACTIONf_chiral_restr0.057468
X-RAY DIFFRACTIONf_plane_restr0.006516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6964-1.73880.31631300.25632454X-RAY DIFFRACTION96
1.7388-1.78580.30611340.24982571X-RAY DIFFRACTION100
1.7858-1.83830.3021360.25092569X-RAY DIFFRACTION100
1.8383-1.89770.27431340.24122543X-RAY DIFFRACTION100
1.8977-1.96550.27161340.2382557X-RAY DIFFRACTION100
1.9655-2.04410.31091350.22962560X-RAY DIFFRACTION100
2.0441-2.13710.28711360.22942567X-RAY DIFFRACTION100
2.1371-2.24980.29231350.21782575X-RAY DIFFRACTION100
2.2498-2.39060.26021350.21752578X-RAY DIFFRACTION100
2.3906-2.57510.25161360.21672574X-RAY DIFFRACTION100
2.5751-2.8340.22321370.21842606X-RAY DIFFRACTION100
2.834-3.24350.23391370.19252601X-RAY DIFFRACTION100
3.2435-4.08430.22081380.16822618X-RAY DIFFRACTION100
4.0843-27.23550.1951380.17282642X-RAY DIFFRACTION96

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