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

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Basic information

Entry
Database: PDB / ID: 7xzu
TitleCrystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)-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: 1.6 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

Downloads & links

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Assembly

Deposited unit
A: Ricin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7985
Polymers30,8971
Non-polymers9014
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-20 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.402, 67.402, 140.766
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-IEK / (2S)-2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]-3-phenyl-propanoic acid / (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)-D-tyrosine


Mass: 354.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14N6O4 / 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.: 242 / 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: 52.46 %
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→60.792 Å / Num. all: 43745 / Num. obs: 43745 / % possible obs: 100 % / Redundancy: 12.9 % / Rpim(I) all: 0.012 / Rrim(I) all: 0.044 / Rsym value: 0.043 / Net I/av σ(I): 14 / Net I/σ(I): 34 / Num. measured all: 562488
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
1.6-1.6913.21.1310.78281662550.3191.1751.1312.8100
1.69-1.7912.80.6811.17578459410.1960.710.6814.4100
1.79-1.9112.70.3662.17107456000.1060.3810.3667.8100
1.91-2.0713.40.1874.26979852240.0530.1950.18714.9100
2.07-2.2612.80.1017.66196048370.0290.1060.10125.2100
2.26-2.5312.90.06312.15675943840.0180.0660.06337.3100
2.53-2.9213.30.03918.65209339170.0110.0410.03957.1100
2.92-3.5812.10.02527.34044833510.0070.0260.02587.8100
3.58-5.0612.80.01735.53394626480.0050.0180.017125.5100
5.06-46.92211.20.01536.81781015880.0050.0160.015117.999.8

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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: 1.6→48.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.868 / SU ML: 0.065 / SU R Cruickshank DPI: 0.0908 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 2185 5 %RANDOM
Rwork0.2056 ---
obs0.2063 41476 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.44 Å2 / Biso mean: 28.056 Å2 / Biso min: 16.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.6→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 52 242 2329
Biso mean--31.52 40.47 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192171
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9792970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8315270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33522.857105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24515332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3651522
X-RAY DIFFRACTIONr_chiral_restr0.0810.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211711
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 150 -
Rwork0.284 3018 -
all-3168 -
obs--100 %

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