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- PDB-2r55: Human StAR-related lipid transfer protein 5 -

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Basic information

Entry
Database: PDB / ID: 2r55
TitleHuman StAR-related lipid transfer protein 5
ComponentsStAR-related lipid transfer protein 5
KeywordsTRANSPORT PROTEIN / alpha and beta protein / cholesterol binding / Structural Genomics / Structural Genomics Consortium / SGC / Lipid transport / Lipid-binding / Transport
Function / homology
Function and homology information


cholesterol import / cholesterol transfer activity / cholesterol binding / Recycling of bile acids and salts / cytosol
Similarity search - Function
StAR-related lipid transfer protein 5/6 / 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLehtio, L. / Busam, R.D. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Lehtio, L. / Busam, R.D. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Herman, M.D. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Sagemark, J. / Sundstrom, M. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Persson, C. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2011
Title: Comparative structural analysis of lipid binding START domains.
Authors: Thorsell, A.G. / Lee, W.H. / Persson, C. / Siponen, M.I. / Nilsson, M. / Busam, R.D. / Kotenyova, T. / Schuler, H. / Lehtio, L.
History
DepositionSep 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Aug 30, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: StAR-related lipid transfer protein 5
B: StAR-related lipid transfer protein 5


Theoretical massNumber of molelcules
Total (without water)51,9672
Polymers51,9672
Non-polymers00
Water46826
1
A: StAR-related lipid transfer protein 5


Theoretical massNumber of molelcules
Total (without water)25,9831
Polymers25,9831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: StAR-related lipid transfer protein 5


Theoretical massNumber of molelcules
Total (without water)25,9831
Polymers25,9831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.870, 62.870, 214.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 2 - 213 / Label seq-ID: 20 - 231

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAuthors state that each chain represents a biological monomer.

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Components

#1: Protein StAR-related lipid transfer protein 5 / StARD5 / START domain-containing protein 5


Mass: 25983.459 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STARD5 / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NSY2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.03992 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2006 / Details: mirrors
RadiationMonochromator: Si(111), Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03992 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 16487 / Num. obs: 16487 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.4 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 23.25
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 22.1 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 5.94 / Num. unique all: 1840 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.3.0032refinement
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JSS

1jss


Resolution: 2.5→19.99 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / SU B: 30.63 / SU ML: 0.322 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.943 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27597 1625 10 %RANDOM
Rwork0.2319 ---
all0.23633 14618 --
obs0.23633 14618 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.472 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 0 26 3318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223380
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9474584
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1075410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13323.247154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.3615546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.621524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022594
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.21331
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22257
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.256
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_it0.4391.52127
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.75423372
X-RAY DIFFRACTIONr_scbond_it1.1931423
X-RAY DIFFRACTIONr_scangle_it1.864.51212
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1646 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight thermal0.080.5
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 118 -
Rwork0.308 1056 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2174-0.3724-0.99873.6213-0.935110.4808-0.3090.07610.0712-0.22340.0241-0.1761-0.59991.1660.2849-0.3021-0.1711-0.08920.17970.102-0.467315.39823.6501-5.4924
21.8733-0.1225-0.20282.3206-2.53519.98970.0387-0.1845-0.0603-0.1483-0.3417-0.42540.8052.12770.303-0.28690.1555-0.01860.6130.2418-0.320321.5081-5.40294.4215
32.10710.15840.26982.9761-1.391310.4984-0.1543-0.19840.0035-0.0211-0.1789-0.1413-0.29241.60570.3332-0.399-0.0339-0.03790.33330.0789-0.42418.96121.8142.0006
43.61430.2129-0.88013.41760.964710.4533-0.2721-0.14960.14130.20410.04610.1725-0.5293-1.14990.226-0.31970.1281-0.07340.2183-0.0965-0.468347.47053.643327.8148
52.4278-0.5112-0.61221.45491.714112.02580.0430.2716-0.1550.0766-0.28110.30090.8957-2.33520.2381-0.2749-0.2029-0.04460.6381-0.2528-0.335441.363-5.416817.8951
62.97130.04750.13063.35711.211310.0579-0.1530.2442-0.0168-0.01-0.15810.0861-0.3498-1.59210.3111-0.36750.0069-0.05060.2915-0.0746-0.467743.90351.803820.3182
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 6920 - 87
2X-RAY DIFFRACTION2AA70 - 12588 - 143
3X-RAY DIFFRACTION3AA126 - 213144 - 231
4X-RAY DIFFRACTION4BB2 - 6920 - 87
5X-RAY DIFFRACTION5BB70 - 12588 - 143
6X-RAY DIFFRACTION6BB126 - 213144 - 231

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