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- PDB-1ift: RICIN A-CHAIN (RECOMBINANT) -

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Basic information

Entry
Database: PDB / ID: 1ift
TitleRICIN A-CHAIN (RECOMBINANT)
ComponentsRICIN
KeywordsHYDROLASE / GLYCOSIDASE / TOXIN / GLYCOPROTEIN
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: 1.8 Å
AuthorsWeston, S.A. / Tucker, A.D. / Thatcher, D.R. / Derbyshire, D.J. / Pauptit, R.A.
CitationJournal: 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.
History
DepositionJul 5, 1996Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RICIN


Theoretical massNumber of molelcules
Total (without water)29,4571
Polymers29,4571
Non-polymers00
Water1,802100
1
A: RICIN

A: RICIN


Theoretical massNumber of molelcules
Total (without water)58,9152
Polymers58,9152
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)68.700, 68.700, 141.500
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


Mass: 29457.291 Da / Num. of mol.: 1 / Fragment: A CHAIN / Mutation: I1M, F2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / References: UniProt: P02879, rRNA N-glycosylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.875 mg/mlprotein1drop
256.2 mMTris-HCl1drop
30.75 mMEDTA1drop
43.75 mMdithiothreitol1drop
516.7 mMsodium citrate1drop
610 %(v/v)ammonium sulfate1drop
750 mMsodium citrate1reservoir
830 %(v/v)ammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 14.8 Å / Num. obs: 26549 / % possible obs: 90.4 % / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 86.3 % / Rmerge(I) obs: 0.504

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.216 / Rfactor obs: 0.216 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 0 100 2138
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.8
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
Lowest resolution: 14.8 Å / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg3
LS refinement shell
*PLUS
Highest resolution: 0.18 Å / Lowest resolution: 0.19 Å / Rfactor all: 0.35

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