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- PDB-7y07: Crystal structure of Ricin A chain bound with (S)-2-amino-N-(1-hy... -

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Basic information

Entry
Database: PDB / ID: 7y07
TitleCrystal structure of Ricin A chain bound with (S)-2-amino-N-(1-hydroxy-3-phenylpropan-2-yl)-4-oxo-3,4-dihydropteridine-7-carboxamide
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: 1.25 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

Downloads & links

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Assembly

Deposited unit
A: Ricin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7705
Polymers30,8971
Non-polymers8734
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-20 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.752, 67.752, 141.397
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-IFX / 2-azanyl-4-oxidanylidene-N-[(2S)-1-oxidanyl-3-phenyl-propan-2-yl]-3H-pteridine-7-carboxamide / (S)-2-amino-N-(1-hydroxy-3-phenylpropan-2-yl)-4-oxo-3,4-dihydropteridine-7-carboxamide


Mass: 340.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16N6O3 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
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: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→61.1 Å / Num. all: 91639 / Num. obs: 91639 / % possible obs: 99.9 % / Redundancy: 11.4 % / Rpim(I) all: 0.01 / Rrim(I) all: 0.036 / Rsym value: 0.035 / Net I/av σ(I): 9.5 / Net I/σ(I): 31.8 / Num. measured all: 1045144
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
1.25-1.325.30.5191.569796130860.2450.5760.5192.899.4
1.32-1.49.80.3692.1122456124920.1230.390.3696100
1.4-1.4913.10.2423.2154245117730.0690.2510.24210.9100
1.49-1.6112.80.1335.8140462110140.0390.1380.13318100
1.61-1.7713.10.0839133168101320.0240.0860.08327.5100
1.77-1.9812.90.0513.811861492080.0140.0520.0542.7100
1.98-2.28130.03518.210669082060.010.0360.03562.1100
2.28-2.813.20.0319.89211069890.0090.0310.0375.1100
2.8-3.9512.50.02720.26865555030.0080.0280.02786.8100
3.95-45.374120.02522.23894832360.0070.0260.02589.899.9

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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: 1.25→47.13 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.817 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0508 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 4613 5 %RANDOM
Rwork0.2261 ---
obs0.2265 86922 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.56 Å2 / Biso mean: 20.053 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å2-0 Å2-0 Å2
2--0.54 Å2-0 Å2
3----1.07 Å2
Refinement stepCycle: final / Resolution: 1.25→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 60 271 2390
Biso mean--24.32 31.26 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192189
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.9812988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6125268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67622.571105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86715327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3231523
X-RAY DIFFRACTIONr_chiral_restr0.0770.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211722
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 341 -
Rwork0.304 6255 -
all-6596 -
obs--98.73 %

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