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- PDB-7y05: Crystal structure of Ricin A chain bound with (R)-2-(2-amino-4-ox... -

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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
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
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

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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)31,4294
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

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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-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

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

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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: 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

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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: 1.6→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 %

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