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- PDB-7y08: Crystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-... -

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Basic information

Entry
Database: PDB / ID: 7y08
TitleCrystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanine
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

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Assembly

Deposited unit
A: Ricin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5004
Polymers30,8971
Non-polymers6033
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.288, 67.288, 141.017
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-RS8 / N-[(2-amino-4-oxo-1,4-dihydropteridin-7-yl)carbonyl]glycyl-L-phenylalanine


Type: peptide-like / Mass: 411.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17N7O5 / 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.: 303 / 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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Ammonium sulfate, Sodium malonate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→60.729 Å / Num. all: 88699 / Num. obs: 88699 / % possible obs: 98.5 % / Redundancy: 13.4 % / Rpim(I) all: 0.015 / Rrim(I) all: 0.055 / Rsym value: 0.053 / Net I/av σ(I): 7.6 / Net I/σ(I): 29.2 / Num. measured all: 1188785
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
1.25-1.325.70.3332.471080124110.1450.3660.3334.696
1.32-1.410.10.2453.2123990122750.080.2580.2458.9100
1.4-1.4915.70.1784.3182599115960.0460.1840.17815.7100
1.49-1.6115.90.1116.8172374108220.0290.1150.11123.3100
1.61-1.77160.0789.216000699890.020.080.07831.6100
1.77-1.98160.05511.414544990670.0140.0570.05542.8100
1.98-2.28160.0461312851780410.0120.0470.04654.4100
2.28-2.815.80.04313.310907568970.0110.0450.04359.9100
2.8-3.9513.60.04513.57045151620.0140.0470.04559.695.6
3.95-45.08310.40.047132524424390.0160.0510.04751.377.4

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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→45.08 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.926 / SU B: 0.753 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 4428 5 %RANDOM
Rwork0.2356 ---
obs0.2364 84163 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.55 Å2 / Biso mean: 17.855 Å2 / Biso min: 9.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-0 Å2-0 Å2
2--0.38 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: final / Resolution: 1.25→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 40 304 2398
Biso mean--20.28 29.99 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192155
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.9712941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0655265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81622.692104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25715325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7261522
X-RAY DIFFRACTIONr_chiral_restr0.0770.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211693
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 312 -
Rwork0.281 5743 -
all-6055 -
obs--92.8 %

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