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- PDB-6ovp: Sterol Carrier Protein 2 from Yarrowia Lipolytica (apo form) -

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Basic information

Entry
Database: PDB / ID: 6ovp
TitleSterol Carrier Protein 2 from Yarrowia Lipolytica (apo form)
ComponentsFatty acid-binding protein
KeywordsLIPID BINDING PROTEIN / NON SPECIFIC LIPID TRANSFER / LONG CHAIN FATTY ACIDS AND COA ESTERS
Function / homology
Function and homology information


peroxisome / lipid binding / cytosol
Similarity search - Function
Lipid-binding protein POX18/UbiT/NSL-TP1 / SCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Fatty acid-binding protein
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.991 Å
AuthorsGianotti, A.R. / Klinke, S. / Ermacora, M.R.
Funding support Argentina, 1items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT 2016-0584 Argentina
CitationJournal: J.Struct.Biol. / Year: 2020
Title: The structure of unliganded sterol carrier protein 2 from Yarrowia lipolytica unveils a mechanism for binding site occlusion.
Authors: Gianotti, A.R. / Klinke, S. / Ermacora, M.R.
History
DepositionMay 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 23, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein
B: Fatty acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2053
Polymers28,1102
Non-polymers951
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-11 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.920, 67.920, 117.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Fatty acid-binding protein / Sterol carrier protein 2 / YLSCP2


Mass: 14055.079 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: SCP2, YALI0E01298g / Variant: CX-121-1B / Plasmid: PET9B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P80547
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.77 Å3/Da / Density % sol: 55.63 % / Description: Diamond-shaped crystals
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: HEPES 0.1 M, sodium citrate 1.4 M, pH 6.5-7.0 / PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2019
Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.99→41.49 Å / Num. obs: 21964 / % possible obs: 99.7 % / Redundancy: 19.7 % / Biso Wilson estimate: 64 Å2 / CC1/2: 1 / Rrim(I) all: 0.054 / Net I/σ(I): 27.9
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 20.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3422 / CC1/2: 0.57 / Rrim(I) all: 2.585 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4JGX

4jgx


Resolution: 1.991→41.486 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.98
RfactorNum. reflection% reflectionSelection details
Rfree0.2932 1095 5 %RANDOM
Rwork0.2409 ---
obs0.2433 21904 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 67 Å2
Refinement stepCycle: LAST / Resolution: 1.991→41.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 5 10 1893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011908
X-RAY DIFFRACTIONf_angle_d1.3552553
X-RAY DIFFRACTIONf_dihedral_angle_d8.1041405
X-RAY DIFFRACTIONf_chiral_restr0.073286
X-RAY DIFFRACTIONf_plane_restr0.008330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9914-2.0820.39531300.36722474X-RAY DIFFRACTION97
2.082-2.19180.38351350.32232568X-RAY DIFFRACTION100
2.1918-2.32910.3581350.30722570X-RAY DIFFRACTION100
2.3291-2.50890.35771360.30122583X-RAY DIFFRACTION100
2.5089-2.76130.32381360.3062589X-RAY DIFFRACTION100
2.7613-3.16080.36091380.28292610X-RAY DIFFRACTION100
3.1608-3.98170.25781390.23652658X-RAY DIFFRACTION100
3.9817-41.49470.26981460.2052757X-RAY DIFFRACTION100

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