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- PDB-3rby: Crystal structure of uncharacterized protein YLR301w from Sacchar... -

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Basic information

Entry
Database: PDB / ID: 3rby
TitleCrystal structure of uncharacterized protein YLR301w from Saccharomycces cerevisiae
ComponentsUncharacterized protein YLR301W
KeywordsUNKNOWN FUNCTION / uncharacterized / beta-barrel
Function / homology
Function and homology information


protein targeting to membrane / endoplasmic reticulum membrane / nucleus / cytosol
Similarity search - Function
Protein HRI1, C-terminal domain / Protein HRI1, N-terminal domain / Protein Hri1 / Hri1, N-terminal / Hri1, N-terminal domain superfamily / Protein HRI1 / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Protein HRI1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.301 Å
AuthorsKim, K.-H. / Kim, E.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Novel beta-structure of YLR301w from Saccharomyces cerevisiae.
Authors: Kim, K.H. / Ahn, H.J. / Lee, W.K. / Lee, C. / Yu, M.H. / Kim, E.E.
History
DepositionMar 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YLR301W
B: Uncharacterized protein YLR301W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3659
Polymers55,3682
Non-polymers9977
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-14 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.320, 122.320, 174.001
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Uncharacterized protein YLR301W


Mass: 27683.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YLR301W / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05905
#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 33% PEGMME 550, 0.1M HEPES, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A10.97939
SYNCHROTRONPAL/PLS 4A21
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDDec 15, 2007mirrors
ADSC QUANTUM 2102CCDMar 20, 2008mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979391
211
ReflectionResolution: 2.3→50 Å / Num. obs: 34825 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 27.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 3.3 / % possible all: 97.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.301→40.24 Å / SU ML: 0.29 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 2000 5.87 %
Rwork0.2039 --
obs0.2064 34058 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.953 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8527 Å2-0 Å2-0 Å2
2--2.8527 Å20 Å2
3----5.7054 Å2
Refinement stepCycle: LAST / Resolution: 2.301→40.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 65 146 4127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094080
X-RAY DIFFRACTIONf_angle_d1.1995526
X-RAY DIFFRACTIONf_dihedral_angle_d20.9831492
X-RAY DIFFRACTIONf_chiral_restr0.088590
X-RAY DIFFRACTIONf_plane_restr0.005716
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.301-2.35860.31971390.265223398
2.3586-2.42230.31351390.25221797
2.4223-2.49360.29551400.2561224498
2.4936-2.57410.31461380.2442222998
2.5741-2.6660.26911410.2468225698
2.666-2.77280.30911410.2442224398
2.7728-2.89890.331400.2459226698
2.8989-3.05170.2811430.246228198
3.0517-3.24280.2891420.2369227799
3.2428-3.49310.2971450.2301232299
3.4931-3.84440.22691450.1968231699
3.8444-4.40010.19961450.1648233099
4.4001-5.54130.18331470.1567235798
5.5413-40.24570.22631550.1857248797

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