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- PDB-8i7p: Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3... -

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Basic information

Entry
Database: PDB / ID: 8i7p
TitleCrystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-tyrosine
Components
  • 6-(2-ethyl-4-hydroxyphenyl)-1H-indazole-3-carboxamide
  • Ricin A chain
KeywordsHYDROLASE / Toxin / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGoto, M. / Sakamoto, N. / Higashi, S. / Kawata, R. / Nagatsu, K. / Saito, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19K05699 Japan
CitationJournal: J Enzyme Inhib Med Chem / Year: 2023
Title: Crystal structure of ricin toxin A chain complexed with a highly potent pterin-based small-molecular inhibitor.
Authors: Goto, M. / Sakamoto, N. / Higashi, S. / Kawata, R. / Nagatsu, K. / Saito, R.
History
DepositionFeb 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin A chain
B: 6-(2-ethyl-4-hydroxyphenyl)-1H-indazole-3-carboxamide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5164
Polymers31,3242
Non-polymers1922
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.803, 67.803, 141.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: Protein/peptide 6-(2-ethyl-4-hydroxyphenyl)-1H-indazole-3-carboxamide


Mass: 427.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG2000, 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: 1.6→48.93 Å / Num. obs: 43942 / % possible obs: 99.2 % / Redundancy: 13 % / CC1/2: 1 / Rpim(I) all: 0.012 / Rrim(I) all: 0.042 / Net I/σ(I): 35.6 / Num. measured all: 571567
Reflection shellResolution: 1.6→1.69 Å / % possible obs: 98.3 % / Redundancy: 13.6 % / Num. measured all: 84549 / Num. unique obs: 6237 / CC1/2: 0.912 / Rpim(I) all: 0.214 / Rrim(I) all: 0.801 / Net I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.93 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.72 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23235 2191 5 %RANDOM
Rwork0.21471 ---
obs0.21563 41706 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.051 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å2-0 Å2-0 Å2
2--0.57 Å2-0 Å2
3----1.14 Å2
Refinement stepCycle: 1 / Resolution: 1.6→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 41 235 2311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192149
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.972937
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.855266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21722.925106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32515327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9151522
X-RAY DIFFRACTIONr_chiral_restr0.0790.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211695
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8432.3831046
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4093.5661306
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2192.5641103
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.46121.3173555
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 135 -
Rwork0.268 2995 -
obs--97.84 %

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