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- PDB-4mj7: Crystal structure of the PIN domain of Saccharomyces cerevisiae Utp23 -

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Basic information

Entry
Database: PDB / ID: 4mj7
TitleCrystal structure of the PIN domain of Saccharomyces cerevisiae Utp23
ComponentsrRNA-processing protein UTP23
KeywordsRNA BINDING PROTEIN / PIN domain / Ribosome synthesis / 90S preribosome / Nucleolus
Function / homology
Function and homology information


endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / small ribosomal subunit rRNA binding / nucleolus / mitochondrion / nucleoplasm
Similarity search - Function
rRNA-processing protein Fcf1/Utp23 / Fcf1 / 5'-nuclease / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
rRNA-processing protein UTP23
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsLu, J. / Ye, K.
CitationJournal: Rna / Year: 2013
Title: Structural and functional analysis of Utp23, a yeast ribosome synthesis factor with degenerate PIN domain
Authors: Lu, J. / Sun, M. / Ye, K.
History
DepositionSep 3, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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: rRNA-processing protein UTP23
B: rRNA-processing protein UTP23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5494
Polymers36,4182
Non-polymers1312
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-28 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.427, 91.427, 92.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein rRNA-processing protein UTP23 / U three protein 23 / U3 small nucleolar RNA-associated protein 23 / U3 snoRNA-associated protein 23


Mass: 18209.143 Da / Num. of mol.: 2 / Fragment: UNP residues 1-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: UTP23, YOR004W / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12339
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 2%(v/v) tacsimate, 20%(w/v) polyethylene glycol 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97637 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97637 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 15536 / % possible obs: 99.6 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 30.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.51→19.929 Å / SU ML: 0.4 / σ(F): 1.1 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2881 771 5.01 %Random
Rwork0.2275 ---
obs0.2304 15380 98.51 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.218 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.8084 Å20 Å2-0 Å2
2--0.8084 Å20 Å2
3----1.6167 Å2
Refinement stepCycle: LAST / Resolution: 2.51→19.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2471 0 2 21 2494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092508
X-RAY DIFFRACTIONf_angle_d1.2583379
X-RAY DIFFRACTIONf_dihedral_angle_d18.943974
X-RAY DIFFRACTIONf_chiral_restr0.091388
X-RAY DIFFRACTIONf_plane_restr0.004436
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.51-2.66690.40911110.3306239798
2.6669-2.87230.38431480.30542410100
2.8723-3.16030.34241390.2763243099
3.1603-3.61530.33011350.2387238798
3.6153-4.54590.25131190.2003243998
4.5459-19.92990.21151190.1825254698

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