[English] 日本語
Yorodumi
- PDB-7y05: Crystal structure of Ricin A chain bound with (R)-2-(2-amino-4-ox... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7y05
TitleCrystal structure of Ricin A chain bound with (R)-2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)-2-phenylacetic acid
ComponentsRicin A chain
KeywordsHYDROLASE / HYDROLASE INHIBITOR
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
Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ricin-type beta-trefoil lectin domain / 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 ...Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ricin-type beta-trefoil lectin domain / 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
Similarity search - Domain/homology
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsGoto, M. / Higashi, S. / Ohba, T. / Kawata, R. / Nagatsu, K. / Suzuki, S. / Saito, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19K05699 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket.
Authors: Goto, M. / Higashi, S. / Ohba, T. / Kawata, R. / Nagatsu, K. / Suzuki, S. / Anslyn, E.V. / Saito, R.
History
DepositionJun 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ricin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4294
Polymers30,8971
Non-polymers5323
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.448, 67.448, 140.959
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Ricin A chain / rRNA N-glycosidase


Mass: 30896.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical ChemComp-IFH / (2R)-2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]-2-phenyl-ethanoic acid / (R)-2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)-2-phenylacetic acid


Mass: 340.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12N6O4 / Feature type: SUBJECT OF INVESTIGATION
#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.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG 2000, Lithium sulfate, Sodium acetate

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→60.842 Å / Num. all: 43853 / Num. obs: 43853 / % possible obs: 100 % / Redundancy: 11.3 % / Rpim(I) all: 0.018 / Rrim(I) all: 0.062 / Rsym value: 0.06 / Net I/av σ(I): 8.2 / Net I/σ(I): 24.5 / Num. measured all: 497134
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.6-1.696.10.4931.53815362630.2150.540.4933.299.9
1.69-1.799.90.3622.15874959530.1210.3820.3626.3100
1.79-1.9113.10.2273.37365756290.0650.2370.22711.5100
1.91-2.0712.50.135.76532352250.0380.1360.1318.3100
2.07-2.2613.20.0858.76400948530.0240.0880.08526.3100
2.26-2.5312.30.06810.25407844010.020.0710.06832.1100
2.53-2.9212.90.05212.95062039160.0150.0540.05240.9100
2.92-3.5812.40.04214.24160033650.0120.0440.04251.6100
3.58-5.0612.20.03814.63246326610.0110.040.03860.5100
5.06-47.69311.60.03614.81848215870.0110.0380.03657.399.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
MOLREPphasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HUO

4huo


Resolution: 1.6→48.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.699 / SU ML: 0.06 / SU R Cruickshank DPI: 0.0923 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 2189 5 %RANDOM
Rwork0.2109 ---
obs0.2119 41579 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.97 Å2 / Biso mean: 20.345 Å2 / Biso min: 9.85 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.6→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 25 270 2329
Biso mean--26.67 34.34 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192109
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.9642879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7715261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75622.843102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41115318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0921521
X-RAY DIFFRACTIONr_chiral_restr0.0780.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211652
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 145 -
Rwork0.296 3019 -
all-3164 -
obs--99.78 %

+
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