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- PDB-2vc4: Ricin A-Chain (Recombinant) E177D Mutant -

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Basic information

Entry
Database: PDB / ID: 2vc4
TitleRicin A-Chain (Recombinant) E177D Mutant
ComponentsRICIN A CHAIN
KeywordsHYDROLASE / GLYCOPROTEIN / PLANT DEFENSE / PROTEIN SYNTHESIS INHIBITOR / TOXIN / LECTIN / GLYCOSIDASE
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 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ricin-type beta-trefoil lectin domain / 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 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ricin-type beta-trefoil lectin domain / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsMarsden, C.J. / Fulop, V.
CitationJournal: FEBS J. / Year: 2007
Title: The Isolation and Characterisation of Temperature-Dependent Ricin a Chain Molecules in Saccharomyces Cerevisiae
Authors: Allen, S.C.H. / Moore, K.A.H. / Marsden, C.J. / Fulop, V. / Moffat, K.G. / Lord, J.M. / Ladds, G. / Roberts, L.M.
History
DepositionSep 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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

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Assembly

Deposited unit
A: RICIN A CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2074
Polymers29,9231
Non-polymers2843
Water7,278404
1
A: RICIN A CHAIN
hetero molecules

A: RICIN A CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4148
Polymers59,8452
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_646y+1,x-1,-z+11
Buried area2130 Å2
ΔGint-19.9 kcal/mol
Surface area28810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)67.400, 67.400, 140.700
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 / RICIN / RRNA N-GLYCOSIDASE


Mass: 29922.730 Da / Num. of mol.: 1 / Fragment: RESIDUES 36-302 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 212 TO 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 % / Description: NONE
Crystal growpH: 4.2 / Details: pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0213
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 17, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0213 Å / Relative weight: 1
ReflectionResolution: 1.39→30 Å / Num. obs: 60577 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 41.6
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6.8 / % possible all: 82.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IFT

1ift


Resolution: 1.39→29.49 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.532 / SU ML: 0.031 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2427 4 %RANDOM
Rwork0.182 ---
obs0.183 58150 92.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.39→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 16 404 2498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222137
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9562909
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2035262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49223.084107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0715331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1381521
X-RAY DIFFRACTIONr_chiral_restr0.0950.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021666
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.21052
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21528
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0161.51332
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61122124
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.693887
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1014.5785
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.39→1.43 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.257 170
Rwork0.218 3844
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2453-0.1947-0.0820.27450.1580.2231-0.03960.0290.00530.05880.0104-0.03070.02090.05710.02920.00280.01050.0031-0.0087-0.0014-0.014968.1365-20.971497.2308
20.0607-0.05790.13070.26950.12380.5698-0.03130.00310.00330.0285-0.00190.04750.0281-0.01930.0332-0.0051-0.00660.0097-0.0112-0.0016-0.004252.9634-17.177293.5679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 118
2X-RAY DIFFRACTION2A119 - 267

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