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- PDB-1il5: STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 2,5-DIAMINO-4,6-D... -

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Basic information

Entry
Database: PDB / ID: 1il5
TitleSTRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 2,5-DIAMINO-4,6-DIHYDROXYPYRIMIDINE (DDP)
ComponentsRICIN A CHAIN
KeywordsHYDROLASE / STRUCTURE-BASED DESIGN / TOXIN-INHIBITOR COMPLEX / GLYCOSIDASE / RIBOSOME-INHIBITING PROTEIN
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
2,4-DIAMINO-4,6-DIHYDROXYPYRIMIDINE / Ricin
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMiller, D.J. / Ravikumar, K. / Shen, H. / Suh, J.-K. / Kerwin, S.M. / Robertus, J.D.
CitationJournal: J.Med.Chem. / Year: 2002
Title: Structure-based design and characterization of novel platforms for ricin and shiga toxin inhibition.
Authors: Miller, D.J. / Ravikumar, K. / Shen, H. / Suh, J.K. / Kerwin, S.M. / Robertus, J.D.
History
DepositionMay 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RICIN A CHAIN
B: RICIN A CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0163
Polymers59,8742
Non-polymers1421
Water61334
1
A: RICIN A CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0792
Polymers29,9371
Non-polymers1421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RICIN A CHAIN


Theoretical massNumber of molelcules
Total (without water)29,9371
Polymers29,9371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.070, 65.950, 50.810
Angle α, β, γ (deg.)93.90, 112.40, 84.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein RICIN A CHAIN


Mass: 29936.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical ChemComp-DDP / 2,4-DIAMINO-4,6-DIHYDROXYPYRIMIDINE


Mass: 142.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N4O2 / Details: CHEMICAL SYNTHESIS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.9
Details: PEG 8000, TRIS-HCL, BETA-MERCAPTOETHANOL, EDTA, 2,5-DIAMINO-4,6-DIHYDROXYPYRIMIDINE, pH 8.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Mlsna, D., (1993) Protein Sci., 2, 429.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.2-2.4 mg/mlprotein1drop
275 mMTris-HCl1reservoirpH8.9
310 mMbeta-mercaptoethanol1reservoir
41 mMEDTA1reservoir
54.1 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 12, 2000
RadiationMonochromator: DOUBLE FOCUSSING MIRRORS (NI & PT) + NI FILTER
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 12362 / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.43
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.56 % / Rmerge(I) obs: 0.246 / % possible all: 83.7
Reflection
*PLUS
Num. measured all: 30838
Reflection shell
*PLUS
% possible obs: 83.7 % / Mean I/σ(I) obs: 2.68

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RTC

1rtc


Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.283 553 5.2 %RANDOM
Rwork0.225 ---
obs-10737 --
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 0 10 34 4235
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg1.108
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5.2 % / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS

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