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- PDB-4clc: Crystal structure of Ybr137w protein -

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Basic information

Entry
Database: PDB / ID: 4clc
TitleCrystal structure of Ybr137w protein
Components(UPF0303 PROTEIN ...) x 5
KeywordsPROTEIN TRANSPORT / GET / GET PATHWAY
Function / homology
Function and homology information


TRC complex / post-translational protein targeting to endoplasmic reticulum membrane / cytosol / cytoplasm
Similarity search - Function
YBR137W-like / Haem-degrading domain / Corrinoid adenosyltransferase PduO/GlcC-like / Corrinoid adenosyltransferase PduO/GlcC-like superfamily / Haem degrading protein HbpS-like / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
UPF0303 protein YBR137W
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsYeh, Y.-H. / Lin, T.-W. / Lin, C.-Y. / Hsiao, C.-D.
Citation
Journal: Mol.Cell.Biol. / Year: 2014
Title: Structural and Functional Characterization of Ybr137Wp Implicate its Involvement in the Targeting of Tail-Anchored Proteins to Membranes.
Authors: Yeh, Y. / Lin, T. / Li, Y. / Tung, J. / Lin, C. / Hsiao, C.
#1: Journal: Mol.Cell / Year: 2010
Title: A Chaperone Cascade Sorts Proteins for Posttranslational Membrane Insertion Into the Endoplasmic Reticulum.
Authors: Wang, F. / Brown, E.C. / Mak, G. / Zhuang, J. / Denic, V.
History
DepositionJan 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns_shell
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.3May 8, 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

Downloads & links

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Assembly

Deposited unit
A: UPF0303 PROTEIN YBR137W
B: UPF0303 PROTEIN YBR137W
C: UPF0303 PROTEIN YBR137W
D: UPF0303 PROTEIN YBR137W
E: UPF0303 PROTEIN YBR137W


Theoretical massNumber of molelcules
Total (without water)102,3375
Polymers102,3375
Non-polymers00
Water1,15364
1
A: UPF0303 PROTEIN YBR137W
B: UPF0303 PROTEIN YBR137W
C: UPF0303 PROTEIN YBR137W
D: UPF0303 PROTEIN YBR137W
E: UPF0303 PROTEIN YBR137W

A: UPF0303 PROTEIN YBR137W
B: UPF0303 PROTEIN YBR137W
C: UPF0303 PROTEIN YBR137W
D: UPF0303 PROTEIN YBR137W
E: UPF0303 PROTEIN YBR137W


Theoretical massNumber of molelcules
Total (without water)204,67510
Polymers204,67510
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area24350 Å2
ΔGint-127.1 kcal/mol
Surface area60060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.254, 135.254, 121.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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UPF0303 PROTEIN ... , 5 types, 5 molecules ABCDE

#1: Protein UPF0303 PROTEIN YBR137W


Mass: 20495.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38276
#2: Protein UPF0303 PROTEIN YBR137W


Mass: 20397.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38276
#3: Protein UPF0303 PROTEIN YBR137W


Mass: 20481.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38276
#4: Protein UPF0303 PROTEIN YBR137W


Mass: 20480.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38276
#5: Protein UPF0303 PROTEIN YBR137W


Mass: 20483.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38276

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Non-polymers , 1 types, 64 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 50

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / Details: 0.1M TRIS-HCL PH8, 0 30% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.5418
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 30600 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 60.94 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 33.8
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 6.8 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.8→26.964 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 29.75 / Stereochemistry target values: ML
Details: MANY RESIDUES WERE REPLACED TO ALA OR GLYCINE DUE TO THEIR POOR ELECTRON DENSITY MAP. IN ADDITION, C-TERMINAL LENGTH OF YBR137WP IN THIS STRUCTURE, WE JUST TRACED TO 169-173.
RfactorNum. reflection% reflection
Rfree0.2678 1992 6.5 %
Rwork0.2068 --
obs0.2108 30592 95.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→26.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6593 0 0 64 6657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096743
X-RAY DIFFRACTIONf_angle_d1.3639130
X-RAY DIFFRACTIONf_dihedral_angle_d14.5562387
X-RAY DIFFRACTIONf_chiral_restr0.0551009
X-RAY DIFFRACTIONf_plane_restr0.0071183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8003-2.87030.38031390.31932037X-RAY DIFFRACTION96
2.8703-2.94780.38571420.31232035X-RAY DIFFRACTION97
2.9478-3.03440.39271420.28982057X-RAY DIFFRACTION97
3.0344-3.13220.34061440.26652058X-RAY DIFFRACTION97
3.1322-3.2440.35031430.2612038X-RAY DIFFRACTION97
3.244-3.37360.33931450.23782053X-RAY DIFFRACTION97
3.3736-3.52690.28841420.21822030X-RAY DIFFRACTION97
3.5269-3.71240.24471450.19862051X-RAY DIFFRACTION96
3.7124-3.94430.30171420.19082030X-RAY DIFFRACTION96
3.9443-4.24770.21951380.18072052X-RAY DIFFRACTION96
4.2477-4.67320.20041450.16052012X-RAY DIFFRACTION94
4.6732-5.34490.22671410.17412037X-RAY DIFFRACTION94
5.3449-6.71670.26011420.21522049X-RAY DIFFRACTION94
6.7167-26.96540.23771420.18492061X-RAY DIFFRACTION91

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