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- PDB-5z2n: Structure of Orp1L N-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 5z2n
TitleStructure of Orp1L N-terminal Domain
ComponentsOxysterol-binding protein-related protein 1
KeywordsENDOCYTOSIS / GTPase / Effector / Complex
Function / homology
Function and homology information


organelle membrane contact site / Synthesis of bile acids and bile salts / : / sterol binding / MHC class II antigen presentation / cholesterol binding / late endosome / endosome / intracellular membrane-bounded organelle / membrane / cytosol
Similarity search - Function
Ankyrin repeats (many copies) / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / Ankyrin repeat-containing domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain ...Ankyrin repeats (many copies) / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / Ankyrin repeat-containing domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / PH-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Oxysterol-binding protein-related protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsMa, X.L. / Liu, K. / Li, J. / Li, H.H. / Li, J. / Yang, C.L. / Liang, H.H.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: A non-canonical GTPase interaction enables ORP1L-Rab7-RILP complex formation and late endosome positioning.
Authors: Ma, X. / Liu, K. / Li, J. / Li, H. / Li, J. / Liu, Y. / Yang, C. / Liang, H.
History
DepositionJan 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
B: Oxysterol-binding protein-related protein 1
A: Oxysterol-binding protein-related protein 1


Theoretical massNumber of molelcules
Total (without water)30,2122
Polymers30,2122
Non-polymers00
Water66737
1
A: Oxysterol-binding protein-related protein 1


Theoretical massNumber of molelcules
Total (without water)15,1061
Polymers15,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxysterol-binding protein-related protein 1


Theoretical massNumber of molelcules
Total (without water)15,1061
Polymers15,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.193, 30.061, 95.055
Angle α, β, γ (deg.)90.00, 126.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Oxysterol-binding protein-related protein 1 / OSBP-related protein 1


Mass: 15106.226 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Osbpl1a, Orp1, Orp1a, Orp1l / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q91XL9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Description: The entry contains friedel pairs in F_plus/minus columns
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M NaCl, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→46.3 Å / Num. obs: 28304 / % possible obs: 93.5 % / Redundancy: 3.4 % / CC1/2: 1 / Net I/σ(I): 18.57
Reflection shellResolution: 2.14→2.27 Å / Mean I/σ(I) obs: 2.23 / CC1/2: 0.943

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K5B

4k5b


Resolution: 2.14→46.276 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 35.94 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2399 1417 5.01 %
Rwork0.2384 --
obs0.2385 28304 93.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→46.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 0 37 2120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062108
X-RAY DIFFRACTIONf_angle_d0.7432837
X-RAY DIFFRACTIONf_dihedral_angle_d17.098791
X-RAY DIFFRACTIONf_chiral_restr0.046325
X-RAY DIFFRACTIONf_plane_restr0.004371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1404-2.21690.44051260.39892400X-RAY DIFFRACTION85
2.2169-2.30570.43141500.3692780X-RAY DIFFRACTION95
2.3057-2.41060.34871400.30932713X-RAY DIFFRACTION96
2.4106-2.53770.31781490.29872779X-RAY DIFFRACTION96
2.5377-2.69670.32221430.28892736X-RAY DIFFRACTION96
2.6967-2.90490.29151410.28222707X-RAY DIFFRACTION96
2.9049-3.19720.32751430.27282716X-RAY DIFFRACTION94
3.1972-3.65960.25941410.24262696X-RAY DIFFRACTION95
3.6596-4.61010.18721370.22644X-RAY DIFFRACTION92
4.6101-46.28690.16461470.18932716X-RAY DIFFRACTION94

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