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- PDB-5yz4: Structure of the PIN domain endonuclease Utp24 -

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Basic information

Entry
Database: PDB / ID: 5yz4
TitleStructure of the PIN domain endonuclease Utp24
ComponentsrRNA-processing protein fcf1
KeywordsHYDROLASE / PIN domain / ribonuclease
Function / homology
Function and homology information


Major pathway of rRNA processing in the nucleolus and cytosol / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / RNA endonuclease activity / small-subunit processome / nucleolus / nucleus
Similarity search - Function
rRNA-processing protein Fcf1/Utp23 / Fcf1 / Large family of predicted nucleotide-binding domains / PIN domain / PIN-like domain superfamily
Similarity search - Domain/homology
rRNA-processing protein fcf1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.135 Å
AuthorsDu, Y. / An, W. / Ye, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31430024 China
CitationJournal: Plos One / Year: 2018
Title: Structural and functional analysis of Utp24, an endonuclease for processing 18S ribosomal RNA.
Authors: An, W. / Du, Y. / Ye, K.
History
DepositionDec 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 2.0Feb 27, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_keywords / struct_ref / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity.pdbx_fragment / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: rRNA-processing protein fcf1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4753
Polymers15,3691
Non-polymers1052
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-10 kcal/mol
Surface area7570 Å2
Unit cell
Length a, b, c (Å)48.740, 73.328, 74.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-201-

CA

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Components

#1: Protein rRNA-processing protein fcf1


Mass: 15369.198 Da / Num. of mol.: 1 / Fragment: UNP residues 60-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972h- / Gene: fcf1 / Production host: Escherichia coli (E. coli) / References: UniProt: O13610
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.16 Å3/Da / Density % sol: 43.02 % / Description: Cluster
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M calcium acetate and 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979135 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979135 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 7270 / % possible obs: 94.5 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.184 / Net I/σ(I): 18.9
Reflection shellResolution: 2.13→2.17 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 284 / CC1/2: 0.795 / % possible all: 73.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MJ7

4mj7


Resolution: 2.135→40.591 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.72
RfactorNum. reflection% reflection
Rfree0.287 668 9.94 %
Rwork0.2219 --
obs0.2282 6721 87.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.135→40.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1072 0 2 14 1088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081090
X-RAY DIFFRACTIONf_angle_d0.9031471
X-RAY DIFFRACTIONf_dihedral_angle_d18.519679
X-RAY DIFFRACTIONf_chiral_restr0.055172
X-RAY DIFFRACTIONf_plane_restr0.012186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1348-2.29960.39681020.283891X-RAY DIFFRACTION66
2.2996-2.5310.3581150.27721088X-RAY DIFFRACTION80
2.531-2.89710.3071370.25961270X-RAY DIFFRACTION92
2.8971-3.64970.27261510.21661359X-RAY DIFFRACTION98
3.6497-40.59850.25481630.19161445X-RAY DIFFRACTION100

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