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- PDB-2r3d: Ricin A-chain (recombinant) complex with Acetamide -

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Basic information

Entry
Database: PDB / ID: 2r3d
TitleRicin A-chain (recombinant) complex with Acetamide
ComponentsRicin A chain (EC 3.2.2.22)
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 / MOLECULAR REPLACEMENT / Resolution: 2.09 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 29, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionNov 20, 2007ID: 1ZB2
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 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 (EC 3.2.2.22)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3194
Polymers30,0681
Non-polymers2513
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.110, 67.110, 141.320
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-409-

HOH

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Components

#1: Protein Ricin A chain (EC 3.2.2.22)


Mass: 30067.953 Da / Num. of mol.: 1 / Fragment: Unp residues 36-302
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-ACM / ACETAMIDE


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER SMART 6000 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→33.784 Å / Num. obs: 22917 / % possible obs: 100 % / Redundancy: 17.9 % / Rsym value: 0.098 / Χ2: 0.83 / Net I/σ(I): 6.72 / Scaling rejects: 2405
Reflection shellResolution: 2→2.09 Å / Mean I/σ(I) obs: 1.36 / Rsym value: 0.451 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
LSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→33.56 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2064516.5 / 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
Rfree0.272 1015 5.1 %RANDOM
Rwork0.234 ---
obs-19857 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.82 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.85 Å20 Å20 Å2
2--2.85 Å20 Å2
3----5.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.09→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 14 106 2157
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it3.181.5
X-RAY DIFFRACTIONc_mcangle_it3.872
X-RAY DIFFRACTIONc_scbond_it4.442
X-RAY DIFFRACTIONc_scangle_it4.732.5
LS refinement shellResolution: 2.09→2.22 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 167 5.2 %
Rwork0.252 3050 -
all-3217 -
obs--99.8 %
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 DIFFRACTION4ACM.PARACM.TOP
X-RAY DIFFRACTION5

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