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Basic information

Entry
Database: PDB / ID: 5dtc
TitleUBL Structure
ComponentsRibosome biogenesis protein YTM1
KeywordsPROTEIN BINDING / ubiquitin
Function / homology:
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRomes, E.M. / Stanley, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Crystal Structure of the Ubiquitin-like Domain of Ribosome Assembly Factor Ytm1 and Characterization of Its Interaction with the AAA-ATPase Midasin.
Authors: Romes, E.M. / Sobhany, M. / Stanley, R.E.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 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: Ribosome biogenesis protein YTM1
B: Ribosome biogenesis protein YTM1


Theoretical massNumber of molelcules
Total (without water)20,3012
Polymers20,3012
Non-polymers00
Water2,468137
1
A: Ribosome biogenesis protein YTM1


Theoretical massNumber of molelcules
Total (without water)10,1511
Polymers10,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribosome biogenesis protein YTM1


Theoretical massNumber of molelcules
Total (without water)10,1511
Polymers10,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.298, 37.738, 41.134
Angle α, β, γ (deg.)82.54, 64.31, 69.62
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ribosome biogenesis protein YTM1 /


Mass: 10150.686 Da / Num. of mol.: 2 / Fragment: UNP residues 5-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YJM1133 / Gene: YTM1, H781_YJM1133O00421 / Plasmid: pGST2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: A0A0D4FJ11
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 50 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium cacodylate, 1M Sodium Citrate / PH range: 6.2-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 7, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 47152 / Num. obs: 18667 / % possible obs: 95.3 % / Redundancy: 2.5 % / Net I/σ(I): 9.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.5 / % possible all: 85.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4WJS

4wjs


Resolution: 1.7→37.057 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 942 5.05 %Random selection
Rwork0.175 ---
obs0.1778 18657 95.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→37.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 0 137 1551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061442
X-RAY DIFFRACTIONf_angle_d0.931944
X-RAY DIFFRACTIONf_dihedral_angle_d11.804552
X-RAY DIFFRACTIONf_chiral_restr0.038222
X-RAY DIFFRACTIONf_plane_restr0.004244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.79290.31731280.18862285X-RAY DIFFRACTION86
1.7929-1.90520.24191300.16382476X-RAY DIFFRACTION94
1.9052-2.05230.2261260.14092564X-RAY DIFFRACTION96
2.0523-2.25880.2061430.13912572X-RAY DIFFRACTION97
2.2588-2.58560.22921450.16232601X-RAY DIFFRACTION97
2.5856-3.25730.23661340.18882605X-RAY DIFFRACTION98
3.2573-37.06570.22811360.18852612X-RAY DIFFRACTION98

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