[English] 日本語
Yorodumi
- PDB-1dix: CRYSTAL STRUCTURE OF RNASE LE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dix
TitleCRYSTAL STRUCTURE OF RNASE LE
ComponentsEXTRACELLULAR RIBONUCLEASE LE
KeywordsHYDROLASE / ALPHA PLUS BETA
Function / homology
Function and homology information


ribonuclease T2 / ribonuclease T2 activity / cell wall / RNA catabolic process / RNA endonuclease activity / lyase activity / extracellular space / RNA binding / extracellular region
Similarity search - Function
Ribonuclease T2, eukaryotic / Ribonuclease T2, His active site 1 / Ribonuclease T2 family histidine active site 1. / Ribonuclease T2-like / Ribonuclease T2 family / Ribonuclease Rh; Chain A / Ribonuclease T2-like / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily ...Ribonuclease T2, eukaryotic / Ribonuclease T2, His active site 1 / Ribonuclease T2 family histidine active site 1. / Ribonuclease T2-like / Ribonuclease T2 family / Ribonuclease Rh; Chain A / Ribonuclease T2-like / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Extracellular ribonuclease LE
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.65 Å
AuthorsTanaka, N. / Nakamura, K.T.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of a plant ribonuclease, RNase LE.
Authors: Tanaka, N. / Arai, J. / Inokuchi, N. / Koyama, T. / Ohgi, K. / Irie, M. / Nakamura, K.T.
#1: Journal: Protein Pept.Lett. / Year: 1999
Title: Crystallization and Preliminary X-ray Crystallographic Studies of Ribonuclease LE from Lycopersicon esculentum
Authors: Tanaka, N. / Arai, J. / Inokuchi, N. / Koyama, T. / Ohgi, K. / Irie, M. / Nakamura, K.T.
History
DepositionNov 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EXTRACELLULAR RIBONUCLEASE LE


Theoretical massNumber of molelcules
Total (without water)22,9121
Polymers22,9121
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.02, 78.79, 32.93
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein EXTRACELLULAR RIBONUCLEASE LE


Mass: 22912.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P80022, EC: 3.1.27.1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG1540, CITRATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 41 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 mMcitrate1drop
336 %(w/v)PEG15401reservoir
40.1 Mcitrate1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 31, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→100 Å / Num. all: 144121 / Num. obs: 22385 / % possible obs: 93.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.049
Reflection
*PLUS
Num. measured all: 144121 / Rmerge(I) obs: 0.054

-
Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
RefinementMethod to determine structure: MIR / Resolution: 1.65→40 Å / σ(F): 1 /
RfactorNum. reflection
Rfree0.278 -
Rwork0.219 -
obs-22353
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 0 136 1748
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_planar_d0.0440.05
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 1 / Num. reflection Rfree: 2296 / % reflection Rfree: 10 % / Rfactor obs: 0.219
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