[English] 日本語
Yorodumi
- PDB-1uq5: RICIN A-CHAIN (RECOMBINANT) N122A MUTANT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uq5
TitleRICIN A-CHAIN (RECOMBINANT) N122A MUTANT
ComponentsRICIN
KeywordsHYDROLASE / GLYCOSIDASE / TOXIN / GLYCOPROTEIN
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMarsden, C.J. / Fulop, V.
Citation
Journal: Eur.J.Biochem. / Year: 2004
Title: The Effect of Mutations Surrounding and within the Active Site on the Catalytic Activity of Ricin a Chain
Authors: Marsden, C.J. / Fulop, V. / Day, P. / Lord, J.M.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: X-Ray Structure of Recombinant Ricin A-Chain at 1.8 A Resolution
Authors: Weston, S.A. / Tucker, A.D. / Thatcher, D.R. / Derbyshire, D.J. / Pauptit, R.A.
History
DepositionOct 15, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RICIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6584
Polymers29,4071
Non-polymers2513
Water9,116506
1
A: RICIN
hetero molecules

A: RICIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3178
Polymers58,8142
Non-polymers5026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_646y+1,x-1,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)67.500, 67.500, 140.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2019-

HOH

21A-2055-

HOH

31A-2141-

HOH

41A-2471-

HOH

DetailsTHIS DIMER IS BECAUSE OF CRYSTAL PACKING BUT NONETHELESSGIVES AN INTERESTING RESULT

-
Components

#1: Protein RICIN


Mass: 29407.107 Da / Num. of mol.: 1 / Fragment: A CHAIN, RESIDUES 40-302 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RICINUS COMMUNIS (castor bean) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM101 / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES ASN 157 ALA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 48 %
Crystal growpH: 4.2 / Details: SEE REFERENCE 1, pH 4.20
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.9 / Method: vapor diffusion, hanging drop / Details: Weston, S.A., (1994) J. Mol. Biol., 244, 410.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.875 mg/mlprotein1drop
256.2 mMTris-HCl1drop
30.75 mMEDTA1drop
43.75 mMdithiothreitol1drop
516.7 mMsodium citrate1drop
610 %(v/v)ammonium sulfate1drop
750 mMsodium citrate1reservoir
830 %(v/v)ammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0213
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 17, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0213 Å / Relative weight: 1
ReflectionResolution: 1.4→46 Å / Num. obs: 274010 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 43.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 8.1 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 46 Å / Num. obs: 60829 / Num. measured all: 274010 / Rmerge(I) obs: 0.031
Reflection shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.436 Å / % possible obs: 99.3 % / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 8.1

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IFT

1ift


Resolution: 1.4→46 Å / SU B: 0.776 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.065
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2448 4 %RANDOM
Rwork0.177 ---
obs0.179 58381 93.9 %-
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 14 506 2596
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.059
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg3
LS refinement shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.436 Å / Rfactor Rfree: 0.192 / Num. reflection Rfree: 188 / Rfactor Rwork: 0.176 / Num. reflection Rwork: 4486

+
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