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- PDB-3px9: RTA in complex with N-(furanylmethyl)-7-carbamoyl-pterin -

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Basic information

Entry
Database: PDB / ID: 3px9
TitleRTA in complex with N-(furanylmethyl)-7-carbamoyl-pterin
ComponentsPreproricin
Keywordshydrolase/inhibitor / Ricin / toxin / protein-ligand complex / hydrolase / ribosome inactivating protein / N-glycosidase / pterin / 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-JP3 / Preproricin / Ricin
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsJasheway, K.R. / Robertus, J.D.
CitationJournal: Eur.J.Med.Chem. / Year: 2011
Title: 7-Substituted pterins provide a new direction for ricin A chain inhibitors.
Authors: Pruet, J.M. / Jasheway, K.R. / Manzano, L.A. / Bai, Y. / Anslyn, E.V. / Robertus, J.D.
History
DepositionDec 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Preproricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2222
Polymers28,9361
Non-polymers2861
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.444, 67.328, 49.462
Angle α, β, γ (deg.)90.000, 112.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Preproricin


Mass: 28935.625 Da / Num. of mol.: 1 / Fragment: UNP residues 18-275
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: D6MWP9, UniProt: P02879*PLUS
#2: Chemical ChemComp-JP3 / 2-amino-N-(furan-2-ylmethyl)-4-oxo-3,4-dihydropteridine-7-carboxamide


Mass: 286.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10N6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 4.1% PEG 8000, 75 mM Bicine pH 8.9, 10 mM 2-mercaptoethanol, 1 mM EDTA, VAPOR DIFFUSION, HANGING 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: Jan 1, 2010
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 19711 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Χ2: 2.564 / Net I/σ(I): 23.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.89-1.923.50.4329361.582191.5
1.92-1.963.70.3719591.633194.7
1.96-23.80.3089501.793192.9
2-2.043.80.2649711.912194.3
2.04-2.083.80.2299531.937194.6
2.08-2.133.80.1939632.093192.8
2.13-2.183.80.1659702.212196.3
2.18-2.243.80.1439702.403193.8
2.24-2.313.80.1279802.656196.5
2.31-2.383.80.1159712.625195.2
2.38-2.473.80.110082.647196.6
2.47-2.573.80.099802.922196.4
2.57-2.683.70.0799823.2196.1
2.68-2.823.70.06810093.125196.7
2.82-33.80.0629993.485198
3-3.233.80.05410003.565197.6
3.23-3.563.80.0510093.579197.5
3.56-4.073.80.04410083.272198
4.07-5.133.80.03810352.555198.5
5.13-503.70.02810581.788199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.24 Å33.64 Å
Translation2.24 Å33.64 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→33.67 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2522 / WRfactor Rwork: 0.2043 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8327 / SU B: 4.089 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1735 / SU Rfree: 0.1571 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 1009 5.1 %RANDOM
Rwork0.1948 ---
obs0.1971 19694 95.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.43 Å2 / Biso mean: 38.3797 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å2-0.36 Å2
2---0.88 Å20 Å2
3---1.72 Å2
Refinement stepCycle: LAST / Resolution: 1.89→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 21 56 2118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222107
X-RAY DIFFRACTIONr_bond_other_d00.021906
X-RAY DIFFRACTIONr_angle_refined_deg1.821.962866
X-RAY DIFFRACTIONr_angle_other_deg0.80734392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64623.048105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07415331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6041521
X-RAY DIFFRACTIONr_chiral_restr0.1150.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212386
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
X-RAY DIFFRACTIONr_mcbond_it1.1971.51284
X-RAY DIFFRACTIONr_mcbond_other0.3051.5523
X-RAY DIFFRACTIONr_mcangle_it2.03822076
X-RAY DIFFRACTIONr_scbond_it3.0253823
X-RAY DIFFRACTIONr_scangle_it5.0064.5790
LS refinement shellResolution: 1.89→1.941 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 72 -
Rwork0.301 1277 -
all-1349 -
obs--89.52 %

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