[English] 日本語
Yorodumi
- PDB-1br5: RICIN A CHAIN (RECOMBINANT) COMPLEX WITH NEOPTERIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1br5
TitleRICIN A CHAIN (RECOMBINANT) COMPLEX WITH NEOPTERIN
ComponentsPROTEIN (RICIN)
KeywordsHYDROLASE / GLYCOSIDASE
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.5 Å
AuthorsDay, P. / Yan, X. / Hollis, T. / Svinth, M. / Monzingo, A.F. / Milne, G.W.A. / Robertus, J.D.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Structure-based identification of a ricin inhibitor.
Authors: Yan, X. / Hollis, T. / Svinth, M. / Day, P. / Monzingo, A.F. / Milne, G.W. / Robertus, J.D.
#1: Journal: Protein Sci. / Year: 1993
Title: The Structure of Recombinant Ricin a Chain at 2.3 Angstroms
Authors: Mlsna, D. / Monzingo, A.F. / Katzin, B.J. / Ernst, S. / Robertus, J.D.
#2: Journal: Proteins / Year: 1991
Title: Structure of Ricin A-Chain at 2.5 Angstroms
Authors: Katzin, B.J. / Collins, E.J. / Robertus, J.D.
History
DepositionAug 26, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 2, 1998Provider: 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 / Item: _software.name
Revision 1.4Aug 9, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (RICIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1902
Polymers29,9371
Non-polymers2531
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.810, 68.790, 50.090
Angle α, β, γ (deg.)90.00, 112.83, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein PROTEIN (RICIN) / E.C.3.2.2.22 / RTA


Mass: 29936.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Organ: SEED / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical ChemComp-NEO / NEOPTERIN


Mass: 253.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.8 %
Crystal growpH: 8.9 / Details: pH 8.9
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Robertus, J.D., (1987) J. Biol. Chem., 262, 19.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-2.5 mg/mlprotein1drop
275 mMTris-HCl1reservoir
31 mMEDTA1reservoir
410 mMbeta-mercaptoethanol1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Dec 15, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.24→20 Å / Num. obs: 11996 / % possible obs: 92 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.0717 / Net I/σ(I): 8.3
Reflection shellResolution: 2.24→2.41 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 2.3 / % possible all: 75

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
UCSD-systemdata reduction
UCSD-systemdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1RTC

1rtc


Resolution: 2.5→10 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.194 --
obs0.194 8854 96.3 %
Refine analyzeLuzzati d res low obs: 0 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 18 55 2187
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.255
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.95
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.377
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it22
X-RAY DIFFRACTIONx_scbond_it1.52
X-RAY DIFFRACTIONx_scangle_it22.5
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.242 1038 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM.WATTOPH.WAT
X-RAY DIFFRACTION3PARAM.N2TOPH.N2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.95
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.377
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_scbond_it1.52
X-RAY DIFFRACTIONx_mcangle_it22
X-RAY DIFFRACTIONx_scangle_it22.5
LS refinement shell
*PLUS
Rfactor Rwork: 0.242

+
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