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

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Basic information

Entry
Database: PDB / ID: 4huo
TitleStructure of Ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)-L-phenylalanine
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
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Dec 28, 2016Group: Structure summary
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_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)30,3482
Polymers29,9371
Non-polymers4111
Water7,152397
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)60,6964
Polymers59,8742
Non-polymers8232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area1740 Å2
ΔGint-11 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.999, 67.999, 140.692
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 / Ricin B chain


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-RS8 / N-[(2-amino-4-oxo-1,4-dihydropteridin-7-yl)carbonyl]glycyl-L-phenylalanine


Type: peptide-like / Mass: 411.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17N7O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.72 Å3/Da / Density % sol: 54.72 %
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: 0.9202 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2011
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.52→61.22 Å / Num. obs: 51425 / % possible obs: 99.8 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.098 / Χ2: 1.31 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.52-1.5513.325420.6691100
1.55-1.571425050.7031100
1.57-1.614.225340.67611000.957
1.6-1.6414.225060.69411000.826
1.64-1.6714.225410.72111000.732
1.67-1.7114.325330.78911000.649
1.71-1.7514.225290.84211000.522
1.75-1.814.325390.88411000.445
1.8-1.8614.225540.99511000.355
1.86-1.9213.825521.61911000.34
1.92-1.9814.225431.57611000.273
1.98-2.0614.225661.50211000.191
2.06-2.1614.225621.72411000.166
2.16-2.271125882.44211000.178
2.27-2.4113.425742.05411000.139
2.41-2.61425811.85511000.116
2.6-2.8613.826041.78711000.093
2.86-3.2713.526311.87311000.075
3.27-4.1313.225861.916196.60.063
4.13-5013.228551.16199.80.046

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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: 1.52→61.22 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.29 / SU B: 1.448 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 2587 5.1 %RANDOM
Rwork0.2011 ---
obs0.2025 50859 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.15 Å2 / Biso mean: 23.2333 Å2 / Biso min: 10.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.59 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.52→61.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 30 397 2505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222162
X-RAY DIFFRACTIONr_bond_other_d0.0030.0217
X-RAY DIFFRACTIONr_angle_refined_deg2.2121.9642945
X-RAY DIFFRACTIONr_angle_other_deg1.59335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4635264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88823.148108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26715333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3861521
X-RAY DIFFRACTIONr_chiral_restr0.1620.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211710
X-RAY DIFFRACTIONr_gen_planes_other0.0080.0215
X-RAY DIFFRACTIONr_mcbond_it1.4821.51314
X-RAY DIFFRACTIONr_mcangle_it2.35822128
X-RAY DIFFRACTIONr_scbond_it3.4823848
X-RAY DIFFRACTIONr_scangle_it5.44.5816
LS refinement shellResolution: 1.522→1.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 180 -
Rwork0.263 3526 -
all-3706 -
obs--99.62 %

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