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- PDB-1jss: Crystal structure of the Mus musculus cholesterol-regulated START... -

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Basic information

Entry
Database: PDB / ID: 1jss
TitleCrystal structure of the Mus musculus cholesterol-regulated START protein 4 (StarD4).
Componentscholesterol-regulated START protein 4
KeywordsLIPID BINDING PROTEIN / START domain / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Pregnenolone biosynthesis / intracellular cholesterol transport / cholesterol binding / endoplasmic reticulum / mitochondrion / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsRomanowski, M.J. / Soccio, R.E. / Breslow, J.L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal structure of the Mus musculus cholesterol-regulated START protein 4 (StarD4) containing a StAR-related lipid transfer domain.
Authors: Romanowski, M.J. / Soccio, R.E. / Breslow, J.L. / Burley, S.K.
History
DepositionAug 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: cholesterol-regulated START protein 4
B: cholesterol-regulated START protein 4


Theoretical massNumber of molelcules
Total (without water)51,1602
Polymers51,1602
Non-polymers00
Water5,224290
1
A: cholesterol-regulated START protein 4


Theoretical massNumber of molelcules
Total (without water)25,5801
Polymers25,5801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cholesterol-regulated START protein 4


Theoretical massNumber of molelcules
Total (without water)25,5801
Polymers25,5801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.966, 69.966, 85.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein cholesterol-regulated START protein 4 / STARD4


Mass: 25579.947 Da / Num. of mol.: 2 / Mutation: K41E, V51A
Source method: isolated from a genetically manipulated source
Details: similar to RIKEN cDNA 2310058G22 gene (Mus musculus)
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL-6J / Gene: BC005642; Unigene Cluster: Mm. 31508 / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q99JV5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 11% PEG8000, 22% glycerol, 0.16M magnesium acetate, 0.08M sodium cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMHEPES1droppH7.5
2100 mM1dropKCl
35 mMdithiothreitol1drop
412 mg/mlprotein1drop
50.1 Msodium cacodylate1reservoirpH6.5
60.2 Mmagnesium acetate1reservoir
716 %(w/v)PEG80001reservoir
822 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9791, 0.9795
DetectorType: MARRESEARCH / Detector: CCD / Date: May 25, 2001
Details: Primary Aperture : 7.4 m from source. Be Windows front end: 0.020" thick; 7.1 m from source exit window: 0.010" thick. White X-Ray Beam.
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97951
ReflectionResolution: 2.2→30 Å / Num. all: 46556 / Num. obs: 46556 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 28
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 6.8 / % possible all: 98.3
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Rmerge(I) obs: 0.301

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→28.55 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 535132.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 4543 9.7 %RANDOM
Rwork0.238 ---
all0.2378 46556 --
obs0.238 46556 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4059 Å2 / ksol: 0.364752 e/Å3
Displacement parametersBiso mean: 36.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å23.07 Å20 Å2
2--2.28 Å20 Å2
3----4.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 0 290 3498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 718 9.5 %
Rwork0.273 6827 -
obs--95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Rfactor obs: 0.234 / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
LS refinement shell
*PLUS
Rfactor Rfree: 0.323 / Rfactor Rwork: 0.273

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