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- PDB-4hv7: Structure of ricin A chain bound with N-(N-(pterin-7-yl)carbonylg... -

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Basic information

Entry
Database: PDB / ID: 4hv7
TitleStructure of ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)glycine
ComponentsRicin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / RICIN / PROTEIN-LIGAND COMPLEX / PTERIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / TOXIN / HYDROLASE / RIBOSOME-INACTIVATING PROTEIN / N-GLYCOSIDASE
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 / 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 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / 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 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-19J / MALONIC ACID / Ricin
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.869 Å
AuthorsJasheway, K.R. / Monzingo, A.F. / Saito, R. / Pruet, J.M. / Manzano, L.A. / Wiget, P.A. / Anslyn, E.V. / Robertus, J.D.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Peptide-conjugated pterins as inhibitors of ricin toxin A.
Authors: Saito, R. / Pruet, J.M. / Manzano, L.A. / Jasheway, K. / Monzingo, A.F. / Wiget, P.A. / Kamat, I. / Anslyn, E.V. / Robertus, J.D.
History
DepositionNov 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 1.4Sep 20, 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
X: Ricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4584
Polymers29,9371
Non-polymers5213
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: Ricin
hetero molecules

X: Ricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9168
Polymers59,8742
Non-polymers1,0436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2390 Å2
ΔGint-36 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.196, 68.196, 140.844
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11X-430-

HOH

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Components

#1: Protein Ricin / Ricin A chain / rRNA N-glycosidase / Linker peptide / Ricin B chain


Mass: 29936.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: castor bean / 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-19J / 2-[2-[(2-azanyl-4-oxidanylidene-1H-pteridin-7-yl)carbonylamino]ethanoylamino]ethanoic acid


Type: peptide-like / Mass: 321.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11N7O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.74 Å3/Da / Density % sol: 55.03 %
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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2011
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.869→50 Å / Num. obs: 27776 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 6.3
Reflection shellResolution: 1.89→1.92 Å / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTC

1rtc


Resolution: 1.869→48.99 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8074 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 1393 5.06 %random
Rwork0.2021 ---
obs0.2039 27514 97.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.985 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 78.74 Å2 / Biso mean: 30.792 Å2 / Biso min: 14.05 Å2
Baniso -1Baniso -2Baniso -3
1-4.7408 Å20 Å2-0 Å2
2--4.7408 Å20 Å2
3----9.4816 Å2
Refinement stepCycle: LAST / Resolution: 1.869→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 35 283 2396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072180
X-RAY DIFFRACTIONf_angle_d0.9512971
X-RAY DIFFRACTIONf_chiral_restr0.065325
X-RAY DIFFRACTIONf_plane_restr0.005394
X-RAY DIFFRACTIONf_dihedral_angle_d13.906793
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.869-1.93550.38581050.35641887199272
1.9355-2.0130.2791530.23962635278899
2.013-2.10460.26781340.203326142748100
2.1046-2.21560.24911280.207826702798100
2.2156-2.35440.29091500.22082601275198
2.3544-2.53620.26361540.213126652819100
2.5362-2.79140.23931340.214426702804100
2.7914-3.19520.24971440.211127182862100
3.1952-4.02540.20961460.182227512897100
4.0254-49.00670.20121450.180629103055100

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