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- PDB-2pko: Crystal structure of yeast Urm1 at 1.8 A resolution -

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Basic information

Entry
Database: PDB / ID: 2pko
TitleCrystal structure of yeast Urm1 at 1.8 A resolution
ComponentsUbiquitin-related modifier 1
KeywordsPROTEIN BINDING / Beta Grasp Fold Ubiquitin-like protein
Function / homology
Function and homology information


cell budding / tRNA thio-modification / protein urmylation / tRNA wobble position uridine thiolation / invasive growth in response to glucose limitation / sulfur carrier activity / tRNA wobble uridine modification / protein tag activity / cellular response to oxidative stress / protein homodimerization activity ...cell budding / tRNA thio-modification / protein urmylation / tRNA wobble position uridine thiolation / invasive growth in response to glucose limitation / sulfur carrier activity / tRNA wobble uridine modification / protein tag activity / cellular response to oxidative stress / protein homodimerization activity / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin-related modifier 1 / Urm1 (Ubiquitin related modifier) / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-related modifier 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLee, E.Y. / Lake, M.W. / Schindelin, H.
CitationJournal: Biochemistry / Year: 2008
Title: The sulfurtransferase activity of Uba4 presents a link between ubiquitin-like protein conjugation and activation of sulfur carrier proteins.
Authors: Schmitz, J. / Chowdhury, M.M. / Hanzelmann, P. / Nimtz, M. / Lee, E.Y. / Schindelin, H. / Leimkuhler, S.
History
DepositionApr 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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
A: Ubiquitin-related modifier 1


Theoretical massNumber of molelcules
Total (without water)11,0391
Polymers11,0391
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.871, 62.681, 27.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-152-

HOH

DetailsMonomer with one molecule in the asymetric unit

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Components

#1: Protein Ubiquitin-related modifier 1


Mass: 11039.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: URM1 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P40554
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1.97 Å3/Da / Density % sol: 37.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 33-35% PEG 8000, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 29, 2003
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→19.75 Å / Num. all: 7848 / Num. obs: 7848 / % possible obs: 97.16 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellHighest resolution: 1.8 Å / % possible all: 97.16

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XO3

1xo3


Resolution: 1.8→19.75 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.727 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26295 384 4.7 %RANDOM
Rwork0.18837 ---
all0.19175 8474 --
obs0.19175 7848 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.252 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.163 Å0.157 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms801 0 0 79 880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022813
X-RAY DIFFRACTIONr_bond_other_d0.0010.02750
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.971102
X-RAY DIFFRACTIONr_angle_other_deg0.81331756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.527599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97226.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84815152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.421153
X-RAY DIFFRACTIONr_chiral_restr0.0950.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02895
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02143
X-RAY DIFFRACTIONr_nbd_refined0.2390.2161
X-RAY DIFFRACTIONr_nbd_other0.1780.2758
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2409
X-RAY DIFFRACTIONr_nbtor_other0.0780.2485
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.273
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0420.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.212
X-RAY DIFFRACTIONr_mcbond_it6.4273658
X-RAY DIFFRACTIONr_mcbond_other1.8183209
X-RAY DIFFRACTIONr_mcangle_it6.845820
X-RAY DIFFRACTIONr_scbond_it8.7214349
X-RAY DIFFRACTIONr_scangle_it11.8768282
LS refinement shellResolution: 1.804→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 39 -
Rwork0.268 543 -
obs--96.84 %

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