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- PDB-6l1d: Structure of human StAR-related lipid transfer protein 4 -

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Basic information

Entry
Database: PDB / ID: 6l1d
TitleStructure of human StAR-related lipid transfer protein 4
ComponentsStAR-related lipid transfer protein 4
KeywordsTRANSPORT PROTEIN / STARD4 / lipid transport / sterol / cholesterol / lipid transfer protein
Function / homology
Function and homology information


cholesterol transport involved in cholesterol storage / positive regulation of bile acid biosynthetic process / intracellular cholesterol transport / cholesterol import / positive regulation of cholesterol metabolic process / Pregnenolone biosynthesis / cholesterol transfer activity / cholesterol binding / cytoplasmic vesicle / endoplasmic reticulum ...cholesterol transport involved in cholesterol storage / positive regulation of bile acid biosynthetic process / intracellular cholesterol transport / cholesterol import / positive regulation of cholesterol metabolic process / Pregnenolone biosynthesis / cholesterol transfer activity / cholesterol binding / cytoplasmic vesicle / endoplasmic reticulum / cytoplasm / cytosol
Similarity search - Function
StAR-related lipid transfer protein 4 / 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
StAR-related lipid transfer protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTong, J. / Im, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017R1A2B4004914 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structural analysis of human sterol transfer protein STARD4.
Authors: Tan, L. / Tong, J. / Chun, C. / Im, Y.J.
History
DepositionSep 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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: StAR-related lipid transfer protein 4
B: StAR-related lipid transfer protein 4


Theoretical massNumber of molelcules
Total (without water)47,7702
Polymers47,7702
Non-polymers00
Water8,701483
1
A: StAR-related lipid transfer protein 4


Theoretical massNumber of molelcules
Total (without water)23,8851
Polymers23,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: StAR-related lipid transfer protein 4


Theoretical massNumber of molelcules
Total (without water)23,8851
Polymers23,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.770, 93.770, 73.275
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein StAR-related lipid transfer protein 4 / START domain-containing protein 4 / StARD4


Mass: 23885.002 Da / Num. of mol.: 2 / Mutation: C75S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STARD4 / Plasmid: pHIS2-Thr / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96DR4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 3.5 Å3/Da / Density % sol: 64.86 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1 M Bicine pH 9.0, 30% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 45852 / % possible obs: 98.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 29.19 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 32.5
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2304

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JSS

1jss


Resolution: 1.95→28.75 Å / SU ML: 0.1792 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0001
RfactorNum. reflection% reflection
Rfree0.2165 2320 5.07 %
Rwork0.1878 --
obs0.1892 45739 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.09 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 0 0 483 3720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643319
X-RAY DIFFRACTIONf_angle_d0.7594508
X-RAY DIFFRACTIONf_chiral_restr0.0509488
X-RAY DIFFRACTIONf_plane_restr0.0054575
X-RAY DIFFRACTIONf_dihedral_angle_d7.70671967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.28461300.25872515X-RAY DIFFRACTION97.82
1.99-2.030.26521420.22612565X-RAY DIFFRACTION99.6
2.03-2.080.27361560.23012558X-RAY DIFFRACTION99.3
2.08-2.130.24551420.21092560X-RAY DIFFRACTION99.67
2.13-2.190.22321240.19842569X-RAY DIFFRACTION99.78
2.19-2.250.22421260.20582581X-RAY DIFFRACTION99.34
2.25-2.330.25631480.21362570X-RAY DIFFRACTION99.23
2.33-2.410.26621460.22052585X-RAY DIFFRACTION99.71
2.41-2.50.27231370.21292535X-RAY DIFFRACTION99.26
2.5-2.620.23431280.21032622X-RAY DIFFRACTION99.53
2.62-2.760.26481260.20442584X-RAY DIFFRACTION99.45
2.76-2.930.24741450.21742549X-RAY DIFFRACTION98.97
2.93-3.160.22251420.20412576X-RAY DIFFRACTION99.38
3.16-3.470.23921490.18322591X-RAY DIFFRACTION99.49
3.47-3.970.17371510.16362560X-RAY DIFFRACTION99.05
3.97-50.14681210.14162522X-RAY DIFFRACTION95.8
5-28.750.1891070.17542377X-RAY DIFFRACTION88.09

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