[English] 日本語
Yorodumi
- PDB-1rtu: USTILAGO SPHAEROGENA RIBONUCLEASE U2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rtu
TitleUSTILAGO SPHAEROGENA RIBONUCLEASE U2
ComponentsRIBONUCLEASE U2
KeywordsHYDROLASE / ENDORIBONUCLEASE / BETA-ISOMERIZED ASPARTATE
Function / homology
Function and homology information


ribonuclease U2 / ribonuclease U2 activity / lyase activity / RNA binding / metal ion binding
Similarity search - Function
: / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesUstilago sphaerogena (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNoguchi, S. / Satow, Y. / Uchida, T. / Sasaki, C. / Matsuzaki, T.
CitationJournal: Biochemistry / Year: 1995
Title: Crystal structure of Ustilago sphaerogena ribonuclease U2 at 1.8 A resolution.
Authors: Noguchi, S. / Satow, Y. / Uchida, T. / Sasaki, C. / Matsuzaki, T.
History
DepositionMay 12, 1995Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.4Apr 4, 2018Group: Advisory / Data collection / Other
Category: diffrn_source / pdbx_database_status ...diffrn_source / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_polymer_linkage
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.5Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RIBONUCLEASE U2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4882
Polymers12,3921
Non-polymers961
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.320, 61.270, 34.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein RIBONUCLEASE U2


Mass: 12392.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ustilago sphaerogena (fungus) / References: UniProt: P00654
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Compound detailsASP 45 IS ISOMERIZED TO L-ISOASPARTATE. A PEPTIDE BOND IS FORMED BETWEEN ASP 45 CG AND GLU 46 N.
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: CRYSTALS WERE PREPARED BY HANGING-DROP VAPOUR-DIFFUSION METHOD AT 293 KELVIN FROM A 20 MG/ML PROTEIN SOLUTION CONTAINING 15 MG/ML 2'-DEOXY 2'-FLUORO ADENYLYL-3',5'-CYTIDINE, 0.4M AMMONIUM ...Details: CRYSTALS WERE PREPARED BY HANGING-DROP VAPOUR-DIFFUSION METHOD AT 293 KELVIN FROM A 20 MG/ML PROTEIN SOLUTION CONTAINING 15 MG/ML 2'-DEOXY 2'-FLUORO ADENYLYL-3',5'-CYTIDINE, 0.4M AMMONIUM SULFATE, EQUILIBRATED AGAINST A RESERVOIR OF 0.9M AMMONIUM SULFATE CONTAINING 0.1M ACETATE BUFFER (PH 4.5)., vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
21.5 mg/ml2'-deoxy-2'-fluro ApC1drop
30.9 Mammonium sulfate1drop
40.9 Mammonium sulfate1reservoir
50.1 Macetate1reservoir

-
Data collection

DiffractionMean temperature: 284 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Type: PHOTON FACTORY / Wavelength: 0.9
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 22, 1990 / Details: DOUBLE FOCUSSING MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→12 Å / Num. obs: 9903 / % possible obs: 96.1 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.0342
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 3 % / Rmerge(I) obs: 0.077 / % possible all: 86.4
Reflection
*PLUS
Highest resolution: 1.8 Å / Rmerge(I) obs: 0.044
Reflection shell
*PLUS

-
Processing

Software
NameVersionClassification
OSCMGR(LOCAL VERSION)data collection
TOMOKOdata reduction
MARIKO(LOCAL PROGRAM)data reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
OSC(LOCAL VERSION)data reduction
APROGRAM BY TOMOKOdata scaling
MARIKOdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RNASE T1 (PDB ENTRY 1RNT)

1rnt


Resolution: 1.8→8 Å / σ(F): 0
RfactorNum. reflection% reflection
all0.143 9807 -
obs-9807 96.5 %
Displacement parametersBiso mean: 13.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 5 141 1016
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0280.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.761
X-RAY DIFFRACTIONp_mcangle_it1.2141.5
X-RAY DIFFRACTIONp_scbond_it1.731.5
X-RAY DIFFRACTIONp_scangle_it2.722
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.170.15
X-RAY DIFFRACTIONp_singtor_nbd0.1570.3
X-RAY DIFFRACTIONp_multtor_nbd0.1470.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1730.3
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor12.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more