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- PDB-5h2a: Crystal structure of Osh1 ANK domain from Kluyveromyces lactis -

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Basic information

Entry
Database: PDB / ID: 5h2a
TitleCrystal structure of Osh1 ANK domain from Kluyveromyces lactis
ComponentsKLLA0C04147p
KeywordsLIPID BINDING PROTEIN / oxysterol binding / lipid transfer / ANK NVJ1
Function / homology
Function and homology information


sterol transfer activity / sterol binding / perinuclear endoplasmic reticulum / maintenance of cell polarity / piecemeal microautophagy of the nucleus / exocytosis / endocytosis / nuclear envelope / plasma membrane / cytosol
Similarity search - Function
Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / PH domain / Ankyrin repeat / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain ...Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / PH domain / Ankyrin repeat / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsIm, Y.J. / Manik, M.K. / Yang, H.S. / Tong, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of Korea2014R1A1A1003060 and 2015M2B2A4031729 Korea, Republic Of
CitationJournal: Structure / Year: 2017
Title: Structure of Yeast OSBP-Related Protein Osh1 Reveals Key Determinants for Lipid Transport and Protein Targeting at the Nucleus-Vacuole Junction
Authors: Manik, M.K. / Yang, H. / Tong, J. / Im, Y.J.
History
DepositionOct 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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: KLLA0C04147p
B: KLLA0C04147p


Theoretical massNumber of molelcules
Total (without water)61,3842
Polymers61,3842
Non-polymers00
Water11,079615
1
A: KLLA0C04147p


Theoretical massNumber of molelcules
Total (without water)30,6921
Polymers30,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KLLA0C04147p


Theoretical massNumber of molelcules
Total (without water)30,6921
Polymers30,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-12 kcal/mol
Surface area28790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.463, 189.092, 41.337
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein KLLA0C04147p


Mass: 30692.049 Da / Num. of mol.: 2 / Fragment: UNP residues 10-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_C04147g / Plasmid: modifed pHIS-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6CUK7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: Bicine-HCl pH 9.0, 20% PEG 3350, 0.2M MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 3, 2016
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 57626 / % possible obs: 99.9 % / Redundancy: 9.5 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 47
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 9.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→30.27 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.56
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 2850 4.95 %Random selection
Rwork0.1787 ---
obs0.1805 57553 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 0 0 615 4806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074258
X-RAY DIFFRACTIONf_angle_d0.8065753
X-RAY DIFFRACTIONf_dihedral_angle_d15.9362645
X-RAY DIFFRACTIONf_chiral_restr0.052658
X-RAY DIFFRACTIONf_plane_restr0.005758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9003-1.93310.24691520.21282644X-RAY DIFFRACTION99
1.9331-1.96820.24061260.20362759X-RAY DIFFRACTION100
1.9682-2.00610.25621240.19672652X-RAY DIFFRACTION100
2.0061-2.0470.21751480.18822711X-RAY DIFFRACTION100
2.047-2.09150.22471560.17692694X-RAY DIFFRACTION100
2.0915-2.14010.22181380.1752698X-RAY DIFFRACTION100
2.1401-2.19360.21961330.1752704X-RAY DIFFRACTION100
2.1936-2.25290.19491380.16552694X-RAY DIFFRACTION100
2.2529-2.31920.20671360.16982747X-RAY DIFFRACTION100
2.3192-2.3940.20491360.17662693X-RAY DIFFRACTION100
2.394-2.47960.22141390.18412724X-RAY DIFFRACTION100
2.4796-2.57880.24671430.19382764X-RAY DIFFRACTION100
2.5788-2.69610.21361660.1832671X-RAY DIFFRACTION100
2.6961-2.83810.26111350.19372735X-RAY DIFFRACTION100
2.8381-3.01580.22761720.19532727X-RAY DIFFRACTION100
3.0158-3.24840.21071500.1862748X-RAY DIFFRACTION100
3.2484-3.57480.24111430.17872761X-RAY DIFFRACTION100
3.5748-4.0910.21451270.15922815X-RAY DIFFRACTION100
4.091-5.15010.16821270.15572855X-RAY DIFFRACTION100
5.1501-30.270.18781610.18972907X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 21.9197 Å / Origin y: 80.4299 Å / Origin z: -22.2802 Å
111213212223313233
T0.1205 Å2-0.0048 Å20.0127 Å2-0.1452 Å2-0.0068 Å2--0.1638 Å2
L-0.0045 °20.0598 °20.1488 °2-0.1326 °2-0.0608 °2--0.1689 °2
S-0.0177 Å °0.0514 Å °0.0351 Å °0.0273 Å °-0.0043 Å °-0.01 Å °0.0018 Å °0.0446 Å °-0.0177 Å °
Refinement TLS groupSelection details: all

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