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- PDB-4hv3: Structure of Ricin A chain bound with N-(N-(pterin-7-yl)carbonyl-... -

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Basic information

Entry
Database: PDB / ID: 4hv3
TitleStructure of Ricin A chain bound with N-(N-(pterin-7-yl)carbonyl-L-serinyl)-L-tryptophan
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 / 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
Chem-19L / MALONIC ACID / Ricin
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsRobertus, J.D. / Manzano, L.A. / Jasheway, K.R. / Monzingo, A.F. / Saito, R. / Pruet, J.M. / Wiget, P.A. / Anslyn, E.V.
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 1.3Nov 15, 2017Group: Refinement description / Category: software
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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)30,8535
Polymers30,0681
Non-polymers7854
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.827, 67.827, 140.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 30067.953 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-19L / (2S)-2-[[(2S)-2-[(2-azanyl-4-oxidanylidene-1H-pteridin-7-yl)carbonylamino]-3-oxidanyl-propanoyl]amino]-3-(1H-indol-3-yl)propanoic acid


Type: peptide-like / Mass: 480.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N8O6
#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.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
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: Mar 10, 2012
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: 1.54→61.1 Å / Num. obs: 49375 / % possible obs: 99.7 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.54-1.5712.80.509198.6
1.57-1.612.80.442198.7
1.6-1.6312.80.383198.7
1.63-1.6612.80.321199.2
1.66-1.6912.80.295199.5
1.69-1.7312.80.255199.6
1.73-1.7812.80.208199.6
1.78-1.8312.90.175199.9
1.83-1.8812.90.151199.9
1.88-1.94130.1181100
1.94-2.0113.10.1011100
2.01-2.0913.20.0831100
2.09-2.1813.20.0731100
2.18-2.313.40.0651100
2.3-2.4413.50.0611100
2.44-2.6313.60.0621100
2.63-2.913.50.0611100
2.9-3.3113.60.0521100
3.31-4.1713.40.0351100
4.17-2013.30.029199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTC

1rtc


Resolution: 1.54→61.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.277 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23078 2500 5.1 %RANDOM
Rwork0.19702 ---
obs0.19874 46787 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.55 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.54→61.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 54 221 2397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.022224
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8061.9773027
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9055267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61823.056108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.98315342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0661521
X-RAY DIFFRACTIONr_chiral_restr0.2660.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211751
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6261.51342
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.65722174
X-RAY DIFFRACTIONr_scbond_it3.9693882
X-RAY DIFFRACTIONr_scangle_it6.0554.5853
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.539→1.579 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 161 -
Rwork0.238 3095 -
obs--97.72 %

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