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- PDB-4mx1: Structure of ricin A chain bound with 2-amino-4-oxo-N-(2-(3-pheny... -

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Basic information

Entry
Database: PDB / ID: 4mx1
TitleStructure of ricin A chain bound with 2-amino-4-oxo-N-(2-(3-phenylureido)ethyl)-3,4-dihydropteridine-7-carboxamide
ComponentsRicin A chain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / TOXIN / HYDROLASE / RIBOSOME-INACTIVATING PROTEIN / N-GLYCOSIDASE / PTERIN / 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
Chem-1MX / MALONIC ACID / Ricin
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsRobertus, J.D. / Wiget, P.A. / Manzano, L.A. / Pruet, J.M. / Gao, G. / Saito, R. / Jasheway, K.R. / Monzingo, A.F. / Anslyn, E.V.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Sulfur incorporation generally improves Ricin inhibition in pterin-appended glycine-phenylalanine dipeptide mimics.
Authors: Wiget, P.A. / Manzano, L.A. / Pruet, J.M. / Gao, G. / Saito, R. / Monzingo, A.F. / Jasheway, K.R. / Robertus, J.D. / Anslyn, E.V.
History
DepositionSep 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: 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 A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7405
Polymers30,0681
Non-polymers6734
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.102, 68.102, 140.532
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: 30067.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Organ: seeds / Plasmid: PUTA / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical ChemComp-1MX / 2-amino-4-oxo-N-{2-[(phenylcarbamoyl)amino]ethyl}-3,4-dihydropteridine-7-carboxamide


Mass: 368.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N8O3
#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.: 108 / 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: 2.71 Å3/Da / Density % sol: 54.61 %
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: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2012
RadiationMonochromator: single crystal, cylindrically bent, Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 45334 / % possible obs: 99.9 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.087 / Χ2: 1.179 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.59-1.6212.50.68222170.4751100
1.62-1.6514.10.59622020.5021100
1.65-1.6814.20.51522410.5271100
1.68-1.7114.30.4622310.5591100
1.71-1.7514.30.38722230.5961100
1.75-1.7914.30.33322340.6491100
1.79-1.8414.30.28222390.7231100
1.84-1.8914.30.2422240.8061100
1.89-1.9414.20.23922391.4131100
1.94-214.30.17822631.0681100
2-2.0714.30.14322181.2451100
2.07-2.1614.30.12722621.4071100
2.16-2.2614.10.1322471.8531100
2.26-2.3814.20.10922541.6781100
2.38-2.5214.20.09922881.4781100
2.52-2.7214.20.09622811.5231100
2.72-2.9914.10.10222922.0741100
2.99-3.43140.09423182.3241100
3.43-4.3213.40.06423531.61100
4.32-5013.20.04125080.954199.1

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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: 1.59→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.716 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 2278 5 %RANDOM
Rwork0.2268 ---
obs0.2285 45227 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.86 Å2 / Biso mean: 24.7573 Å2 / Biso min: 10.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.63 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 46 108 2276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222232
X-RAY DIFFRACTIONr_angle_refined_deg2.491.9723039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5815271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15923.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.54315344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8171521
X-RAY DIFFRACTIONr_chiral_restr0.3360.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211761
X-RAY DIFFRACTIONr_mcbond_it1.5991.51348
X-RAY DIFFRACTIONr_mcangle_it2.58722186
X-RAY DIFFRACTIONr_scbond_it3.9793884
X-RAY DIFFRACTIONr_scangle_it6.1314.5851
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 166 -
Rwork0.296 3114 -
all-3280 -
obs--99.39 %

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