[English] 日本語
Yorodumi
- PDB-9rnt: RIBONUCLEASE T1 WITH FREE RECOGNITION AND CATALYTIC SITE: CRYSTAL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rnt
TitleRIBONUCLEASE T1 WITH FREE RECOGNITION AND CATALYTIC SITE: CRYSTAL STRUCTURE ANALYSIS AT 1.5 ANGSTROMS RESOLUTION
ComponentsRIBONUCLEASE T1
KeywordsHYDROLASE(ENDORIBONUCLEASE)
Function / homology
Function and homology information


hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / endonuclease activity / lyase activity / RNA binding
Similarity search - Function
: / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsMartinez-Oyanedel, J. / Heinemann, U. / Saenger, W.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Ribonuclease T1 with free recognition and catalytic site: crystal structure analysis at 1.5 A resolution.
Authors: Martinez-Oyanedel, J. / Choe, H.W. / Heinemann, U. / Saenger, W.
#1: Journal: Biochemistry / Year: 1989
Title: Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding
Authors: Kostrewa, D. / Choe, H.-W. / Heinemann, U. / Saenger, W.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Three-Dimensional Structure of the Ribonuclease T1(Asterisk)2'-Gmp Complex at 1.9-Angstroms Resolution
Authors: Arni, R. / Heinemann, U. / Tokuoka, R. / Saenger, W.
#3: Journal: Nature / Year: 1982
Title: Specific Protein-Nucleic Acid Recognition in Ribonuclease T1-2'-Guanylic Acid Complex. An X-Ray Study
Authors: Heinemann, U. / Saenger, W.
History
DepositionSep 25, 1991Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RIBONUCLEASE T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1352
Polymers11,0951
Non-polymers401
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.730, 46.390, 41.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO 39 AND PRO 55 ARE CIS PROLINES.

-
Components

#1: Protein RIBONUCLEASE T1 /


Mass: 11094.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / References: UniProt: P00651, EC: 3.1.27.3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 %(w/v)protein1drop
235 %(w/v)PEG40001reservoir
35 mMsodium acetate1reservoir
42 mMcalcium acetate1reservoir
520 mMTris acetate1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Num. obs: 13115 / % possible obs: 84.5 % / Num. measured all: 17624 / Rmerge F obs: 1

-
Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.5→6 Å / σ(F): 0 /
RfactorNum. reflection
obs0.143 12632
Refinement stepCycle: LAST / Resolution: 1.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms797 0 1 121 919
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0250.02
X-RAY DIFFRACTIONp_angle_d0.0520.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0630.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.982
X-RAY DIFFRACTIONp_mcangle_it2.693
X-RAY DIFFRACTIONp_scbond_it4.134.5
X-RAY DIFFRACTIONp_scangle_it5.96
X-RAY DIFFRACTIONp_plane_restr0.0150.015
X-RAY DIFFRACTIONp_chiral_restr0.2680.15
X-RAY DIFFRACTIONp_singtor_nbd0.1410.15
X-RAY DIFFRACTIONp_multtor_nbd0.1290.15
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.83
X-RAY DIFFRACTIONp_staggered_tor14.415
X-RAY DIFFRACTIONp_orthonormal_tor2620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
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