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

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Basic information

Entry
Database: PDB / ID: 7xzw
TitleCrystal structure of Ricin A chain bound with (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)-D-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
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: 1.45 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)31,4434
Polymers30,8971
Non-polymers5463
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.164, 67.164, 141.191
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-IEW / (2R)-2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]-3-phenyl-propanoic acid / (2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)-D-phenylalanine


Mass: 354.320 Da / Num. of mol.: 1 / 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.: 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: 2.58 Å3/Da / Density % sol: 52.27 %
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: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→60.651 Å / Num. all: 58196 / Num. obs: 58196 / % possible obs: 100 % / Redundancy: 11.6 % / Rpim(I) all: 0.013 / Rrim(I) all: 0.044 / Rsym value: 0.042 / Net I/av σ(I): 7.9 / Net I/σ(I): 28.6 / Num. measured all: 672461
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
1.45-1.536.90.61.35744983610.2410.6490.62.9100
1.53-1.6211.50.4091.99082479000.1250.4280.4096100
1.62-1.73130.26239688874520.0750.2730.2629.9100
1.73-1.8712.70.1465.38828969650.0420.1520.14616.3100
1.87-2.0513.10.0779.88396264250.0220.080.07728.4100
2.05-2.2912.60.048157341358480.0140.050.04841.9100
2.29-2.6512.80.03718.76620051920.0110.0380.03752.9100
2.65-3.2412.10.0320.15395444530.0090.0320.0364.8100
3.24-4.5911.30.0319.13958835130.0090.0310.0375100
4.59-47.49210.50.036142189420870.0110.0380.03671.899.8

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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: 1.45→48.66 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.289 / SU ML: 0.05 / SU R Cruickshank DPI: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 2940 5.1 %RANDOM
Rwork0.2149 ---
obs0.2164 55159 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.33 Å2 / Biso mean: 24.31 Å2 / Biso min: 13.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.45→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 25 270 2362
Biso mean--26.98 36.79 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192193
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.9633001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6795278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0622.727110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24815341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2771524
X-RAY DIFFRACTIONr_chiral_restr0.080.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211730
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 219 -
Rwork0.281 4025 -
all-4244 -
obs--99.98 %

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