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- PDB-4esi: Structure of ricin A chain bound with N-((1H-1,2,3-triazol-4-yl)m... -

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Basic information

Entry
Database: PDB / ID: 4esi
TitleStructure of ricin A chain bound with N-((1H-1,2,3-triazol-4-yl)methyl-2-amino-4-oxo-3,4-dihydropteridine-7-carboxamide
ComponentsRicin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / RICIN / TOXIN / PROTEIN-LIGAND COMPLEX / HYDROLASE / RIBOSOME INACTIVATING PROTEIN / N-GLYCOSIDASE / PTERIN / HYDROLASE-INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
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 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / 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 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / 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 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsJasheway, K.R. / Pruet, J.M. / Ryoto, S. / Manzano, L.A. / Wiget, P.A. / Kamat, I. / Anslyn, E.V. / Monzingo, A.F. / Robertus, J.D.
CitationJournal: ACS Med Chem Lett / Year: 2012
Title: Optimized 5-membered heterocycle-linked pterins for the inhibition of Ricin Toxin A.
Authors: Pruet, J.M. / Saito, R. / Manzano, L.A. / Jasheway, K.R. / Wiget, P.A. / Kamat, I. / Anslyn, E.V. / Robertus, J.D.
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2242
Polymers29,9371
Non-polymers2871
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.359, 68.359, 141.088
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 / Ricin A chain / rRNA N-glycosidase / Linker peptide


Mass: 29936.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Plasmid: PUTA / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical ChemComp-0RB / 2-amino-4-oxo-N-(1H-1,2,3-triazol-5-ylmethyl)-1,4-dihydropteridine-7-carboxamide


Mass: 287.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9N9O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.3 M ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 29, 2011 / Details: Varimax HF
RadiationMonochromator: Varimax HF optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→61.52 Å / Num. all: 25119 / Num. obs: 25119 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.083 / Χ2: 2.151 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.87-1.95.90.83513191.581194.5
1.9-1.944.60.61710042.421172.3
1.94-1.976.60.53913821.646199.8
1.97-2.016.60.41314211.498199.9
2.01-2.066.50.36813881.778199.9
2.06-2.1160.33513642.553199.1
2.11-2.166.60.25814001.695199.8
2.16-2.226.40.23414101.815199.4
2.22-2.2830.2072871.965120.4
2.28-2.366.60.16913921.976198.7
2.36-2.446.50.1513982.036199.4
2.44-2.546.60.13713912.145198.2
2.54-2.656.40.1213842.386198.3
2.65-2.796.30.10713702.67196.4
2.79-2.976.30.09413412.756193.3
2.97-3.260.08412552.819187.4
3.2-3.525.30.07811573.089180.2
3.52-4.034.20.0686532.876143.9
4.03-5.075.70.05912752.581186.4
5.07-5060.04415281.84194.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTC

1rtc


Resolution: 1.87→61.52 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.195 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2847 1251 5 %RANDOM
Rwork0.229 ---
obs0.2318 24833 87.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.07 Å2 / Biso mean: 37.3891 Å2 / Biso min: 20.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20 Å2
2--1.34 Å20 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 1.87→61.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 21 169 2248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022126
X-RAY DIFFRACTIONr_angle_refined_deg2.0511.9622895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9345260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4823.048105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63515329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4721521
X-RAY DIFFRACTIONr_chiral_restr0.1670.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211666
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.465 70 -
Rwork0.39 1350 -
all-1420 -
obs--74.35 %

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