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- PDB-2r2x: Ricin A-chain (recombinant) complex with Urea -

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Basic information

Entry
Database: PDB / ID: 2r2x
TitleRicin A-chain (recombinant) complex with Urea
ComponentsRicin A chain
KeywordsHYDROLASE / Ricin / Ricinus communis / N-glycosidase / Toxin / Glycoprotein / Lectin / Plant defense / Protein synthesis inhibitor
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: 2.4 Å
AuthorsCarra, J.H. / McHugh, C.A. / Mulligan, S. / Machiesky, L.M. / Soares, A.S. / Millard, C.B.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site.
Authors: Carra, J.H. / McHugh, C.A. / Mulligan, S. / Machiesky, L.M. / Soares, A.S. / Millard, C.B.
History
DepositionAug 28, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionNov 20, 2007ID: 1ZAM
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
SupersessionJul 21, 2009ID: 2PJN
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3204
Polymers30,0681
Non-polymers2523
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.370, 67.370, 141.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-362-

HOH

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Components

#1: Protein Ricin A chain


Mass: 30067.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / 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: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: Ammonium sulfate, sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Apr 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→22.57 Å / Num. obs: 13295 / % possible obs: 99.7 % / Redundancy: 4.37 % / Rmerge(I) obs: 0.114 / Χ2: 0.99 / Net I/σ(I): 8.9 / Scaling rejects: 439
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.4-2.494.440.3733.7575312801.2199.8
2.49-2.594.480.3153.9587813021.06100
2.59-2.74.440.2824.7582212991.299.8
2.7-2.844.470.2215.4587013071.0299.9
2.84-3.024.460.1646.6583713040.9499.9
3.02-3.264.430.1568.2589113220.97100
3.26-3.584.40.09610.8593113360.9299.9
3.58-4.14.270.07313577613340.8699.7
4.1-5.154.280.05817.2590913710.8999.6
5.15-22.574.020.05816581114400.8198.8

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Processing

Software
NameVersionClassificationNB
d*TREK9.2LDzdata scaling
CNS1.1refinement
PDB_EXTRACT3data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→22.57 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1581991.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.297 658 5 %RANDOM
Rwork0.252 ---
obs-13291 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.415 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.29 Å20 Å20 Å2
2--3.29 Å20 Å2
3----6.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→22.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 14 66 2117
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 112 5.2 %
Rwork0.286 2040 -
all-2152 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4UREA.PARUREA.TOP
X-RAY DIFFRACTION5

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