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- PDB-7y4m: Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3... -

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Basic information

Entry
Database: PDB / ID: 7y4m
TitleCrystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanyl-N6-((benzyloxy)carbonyl)-L-lysine
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: 1.45 Å
AuthorsKatakura, S. / Goto, M. / Ohba, T. / Kawata, R. / Nagatsu, K. / Higashi, S. / Matsumoto, K. / Kurisu, K. / Ohtsuka, K. / Saito, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19K05699 Japan
CitationJournal: Plos One / Year: 2022
Title: Pterin-based small molecule inhibitor capable of binding to the secondary pocket in the active site of ricin-toxin A chain.
Authors: Saito, R. / Goto, M. / Katakura, S. / Ohba, T. / Kawata, R. / Nagatsu, K. / Higashi, S. / Kurisu, K. / Matsumoto, K. / Ohtsuka, K.
History
DepositionJun 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ricin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7634
Polymers30,8971
Non-polymers8663
Water4,882271
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.752, 67.752, 141.316
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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-IWQ / (2S)-2-[[(2S)-2-[2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]ethanoylamino]-3-phenyl-propanoyl]amino]-6-(phenylmethoxycarbonylamino)hexanoic acid


Type: peptide-like / Mass: 673.676 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H35N9O8 / 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.: 271 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG 2000, Lithium sulfate, Sodium acetate

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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: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→61.093 Å / Num. all: 59220 / Num. obs: 59220 / % possible obs: 100 % / Redundancy: 12.8 % / Rpim(I) all: 0.009 / Rrim(I) all: 0.032 / Rsym value: 0.031 / Net I/av σ(I): 12.7 / Net I/σ(I): 37.9 / Num. measured all: 760105
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
1.45-1.5312.70.6441.210799784830.1870.670.6444.1100
1.53-1.62130.3782.110441280470.1090.3930.3786.9100
1.62-1.7313.20.2323.410004075860.0660.2420.23211100
1.73-1.8712.60.1256.28922070900.0370.130.12518.7100
1.87-2.0513.40.06711.28761765590.0190.070.06733.7100
2.05-2.2912.80.04117.37608059410.0120.0430.04152.3100
2.29-2.6513.10.03121.66930952970.0090.0320.03169.6100
2.65-3.2412.50.02523.95664845190.0070.0260.02589.3100
3.24-4.5912.50.0229.14485435840.0060.0210.02113.4100
4.59-47.10511.30.01930.32392821140.0060.020.019108.299.8

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Phasing

PhasingMethod: molecular replacement

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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: 1.45→48.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.308 / SU ML: 0.051 / SU R Cruickshank DPI: 0.0743 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 2896 4.9 %RANDOM
Rwork0.222 ---
obs0.223 56232 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.59 Å2 / Biso mean: 27.075 Å2 / Biso min: 13.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0 Å2-0 Å2
2--0.63 Å2-0 Å2
3----1.27 Å2
Refinement stepCycle: final / Resolution: 1.45→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 59 271 2389
Biso mean--29.46 39.48 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192180
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9772973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5815266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81522.692104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25715325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1971522
X-RAY DIFFRACTIONr_chiral_restr0.080.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211714
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 203 -
Rwork0.284 4068 -
all-4271 -
obs--100 %

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