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- PDB-1obs: STRUCTURE OF RICIN A CHAIN MUTANT -

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Basic information

Entry
Database: PDB / ID: 1obs
TitleSTRUCTURE OF RICIN A CHAIN MUTANT
ComponentsRICIN A CHAIN
KeywordsGLYCOSIDASE / HYDROLASE / TOXIN / DUPLICATION / GLYCOPROTEIN / LECTIN
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
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsDay, P.J. / Ernst, S.R. / Frankel, A.E. / Monzingo, A.F. / Pascal, J.M. / Svinth, M. / Robertus, J.D.
Citation
Journal: Biochemistry / Year: 1996
Title: Structure and activity of an active site substitution of ricin A chain.
Authors: Day, P.J. / Ernst, S.R. / Frankel, A.E. / Monzingo, A.F. / Pascal, J.M. / Molina-Svinth, M.C. / Robertus, J.D.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: X-Ray Structure of Recombinant Ricin A-Chain at 1.8 A Resolution
Authors: Weston, S.A. / Tucker, A.D. / Thatcher, D.R. / Derbyshire, D.J. / Pauptit, R.A.
#2: Journal: Protein Sci. / Year: 1993
Title: Structure of Recombinant Ricin a Chain at 2.3 A
Authors: Mlsna, D. / Monzingo, A.F. / Katzin, B.J. / Ernst, S. / Robertus, J.D.
History
DepositionJun 25, 1996Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RICIN A CHAIN


Theoretical massNumber of molelcules
Total (without water)29,9181
Polymers29,9181
Non-polymers00
Water1,56787
1
A: RICIN A CHAIN

A: RICIN A CHAIN


Theoretical massNumber of molelcules
Total (without water)59,8352
Polymers59,8352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_646y+1,x-1,-z+11
Unit cell
Length a, b, c (Å)68.800, 68.800, 141.200
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 A CHAIN


Mass: 29917.711 Da / Num. of mol.: 1 / Mutation: R180H
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlprotein1drop
23 mMphosphate1drop
3100 mMsodium chloride1drop
40.2 Mammonium sulfate1drop
50.03 Msodium acetate1drop
60.5 Mammonium sulfate1reservoir
70.1 Msodium acetate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Mar 6, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 18873 / % possible obs: 90.9 % / Observed criterion σ(I): 0 / Redundancy: 20 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Num. measured all: 379920

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→10 Å / σ(F): 2
Details: SET OF IDEAL BOND LENGTHS AND ANGLES USED DURING REFINEMENT: RAMACHANDRAN ET AL. (1974), BIOCHIM. BIOPHYS. ACTA 359, 298. FINAL RMS COORD. SHIFT 0.49 ANGSTROMS
RfactorNum. reflection% reflection
Rwork0.214 --
obs0.214 17633 99.8 %
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 0 87 2117
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.75
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.82
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.28
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.82
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.28

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