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- PDB-1uq4: RICIN A-CHAIN (RECOMBINANT) R213D MUTANT -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1uq4
TitleRICIN A-CHAIN (RECOMBINANT) R213D MUTANT
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMarsden, C.J. / Fulop, V.
Citation
Journal: Eur.J.Biochem. / Year: 2004
Title: The Effect of Mutations Surrounding and within the Active Site on the Catalytic Activity of Ricin a Chain
Authors: Marsden, C.J. / Fulop, V. / Day, P. / Lord, J.M.
#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.
History
DepositionOct 15, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RICIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6003
Polymers29,4081
Non-polymers1922
Water7,314406
1
A: RICIN
hetero molecules

A: RICIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2006
Polymers58,8162
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_646y+1,x-1,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)67.300, 67.300, 140.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2039-

HOH

21A-2084-

HOH

31A-2374-

HOH

DetailsTHIS DIMER IS BECAUSE OF CRYSTAL PACKING BUT NONETHELESSGIVES AN INTERESTING RESULT

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Components

#1: Protein RICIN


Mass: 29408.029 Da / Num. of mol.: 1 / Fragment: A CHAIN, RESIDUES 40-302 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RICINUS COMMUNIS (castor bean) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM101 / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES ARG 248 ASP

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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: 2.7 Å3/Da / Density % sol: 48 %
Crystal growpH: 4.2 / Details: SEE REFERENCE 1, pH 4.20
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.9 / Method: vapor diffusion, hanging drop / Details: Weston, S.A., (1994) J. Mol. Biol., 244, 410.
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Nov 17, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→28 Å / Num. obs: 53233 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 21.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 4.7 / % possible all: 44
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 28 Å / Num. obs: 22494 / % possible obs: 85.6 % / Num. measured all: 53233 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.949 Å / % possible obs: 43.6 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 4.7

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IFT

1ift


Resolution: 1.9→28 Å / SU B: 3.03 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.159
RfactorNum. reflection% reflectionSelection details
Rfree0.231 921 4 %RANDOM
Rwork0.154 ---
obs0.157 21573 85.6 %-
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--0.68 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 10 406 2492
Refinement
*PLUS
% reflection Rfree: 4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.021
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.257 / Num. reflection Rfree: 24 / Rfactor Rwork: 0.154 / Num. reflection Rwork: 720

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