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- PDB-1rtc: THE STRUCTURE OF RECOMBINANT RICIN A CHAIN AT 2.3 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 1rtc
TitleTHE STRUCTURE OF RECOMBINANT RICIN A CHAIN AT 2.3 ANGSTROMS
ComponentsRICIN
KeywordsGLYCOSIDASE
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: 2.3 Å
AuthorsMlsna, D. / Monzingo, A.F. / Katzin, B.J. / Ernst, S. / Robertus, J.D.
Citation
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.
#1: Journal: Proteins / Year: 1991
Title: Structure of Ricin A-Chain at 2.5 Angstroms
Authors: Katzin, B.J. / Collins, E.J. / Robertus, J.D.
#2: Journal: J.Biol.Chem. / Year: 1987
Title: Crystallization of Ricin a Chain Obtained from a Cloned Gene Expressed in Escherichia Coli
Authors: Robertus, J.D. / Piatak, M. / Ferris, R. / Houston, L.L.
History
DepositionOct 29, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RICIN


Theoretical massNumber of molelcules
Total (without water)30,0681
Polymers30,0681
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.600, 68.100, 50.200
Angle α, β, γ (deg.)90.00, 112.90, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: ILE 1 - PHE 2 OMEGA ANGLE = 213.103 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein RICIN /


Mass: 30067.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Organ: BEAN / References: UniProt: P02879, rRNA N-glycosylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-2.5 mg/mlprotein1drop
275 mMTris-HCl1reservoir
31 mMEDTA1reservoir
410 mMbeta-mercaptoethanol1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 16705 / Num. measured all: 60941 / Rmerge(I) obs: 0.04

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.23 / Rfactor obs: 0.23 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 0 48 2180
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.86
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 2.3 Å / Num. reflection obs: 10973 / Rfactor obs: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.86

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