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- PDB-1em2: Star-related lipid transport domain of MLN64 -

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Basic information

Entry
Database: PDB / ID: 1em2
TitleStar-related lipid transport domain of MLN64
ComponentsMLN64 PROTEIN
KeywordsLIPID BINDING PROTEIN / BETA BARREL
Function / homology
Function and homology information


vesicle tethering to endoplasmic reticulum / progesterone biosynthetic process / endoplasmic reticulum-endosome membrane contact site / organelle membrane contact site / Pregnenolone biosynthesis / cholesterol transfer activity / cholesterol transport / mitochondrial transport / cholesterol binding / steroid metabolic process ...vesicle tethering to endoplasmic reticulum / progesterone biosynthetic process / endoplasmic reticulum-endosome membrane contact site / organelle membrane contact site / Pregnenolone biosynthesis / cholesterol transfer activity / cholesterol transport / mitochondrial transport / cholesterol binding / steroid metabolic process / cholesterol metabolic process / lipid metabolic process / late endosome membrane / endosome / lysosomal membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein homodimerization activity / mitochondrion / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
MENTAL domain / StAR-related lipid transfer protein 3, C-terminal / Cholesterol-capturing domain / MENTAL domain profile. / Steroidogenic acute regulatory protein-like / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain ...MENTAL domain / StAR-related lipid transfer protein 3, C-terminal / Cholesterol-capturing domain / MENTAL domain profile. / Steroidogenic acute regulatory protein-like / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D(-)-TARTARIC ACID / StAR-related lipid transfer protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsTsujishita, Y. / Hurley, J.H.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure and lipid transport mechanism of a StAR-related domain.
Authors: Tsujishita, Y. / Hurley, J.H.
History
DepositionMar 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 3, 2021Group: Atomic model / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MLN64 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2632
Polymers26,1131
Non-polymers1501
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.417, 83.417, 81.946
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-638-

HOH

21A-669-

HOH

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Components

#1: Protein MLN64 PROTEIN


Mass: 26113.141 Da / Num. of mol.: 1 / Fragment: STAR-RELATED DOMAIN / Mutation: F388M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: Q14849
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.15 Å3/Da / Density % sol: 60.96 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: K/Na tartrare, lithium sulfate, CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Temperature: 24 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMCHES1reservoirpH9.5
2950 mMsodium potassium tartrate1reservoir
3200 mM1reservoirLiSO4

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: OTHER / Detector: CCD / Date: Nov 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→25 Å / Rmerge(I) obs: 0.065
Reflection
*PLUS
Num. obs: 16818 / % possible obs: 98.1 % / Num. measured all: 136560

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→25 Å / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.207
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 10 165 1891
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 25 Å / Num. reflection obs: 16818 / % reflection Rfree: 5 % / Rfactor obs: 0.207 / Rfactor Rfree: 0.264
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.85
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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