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- PDB-3hio: Crystal structure of Ricin A-chain in complex with the cyclic tet... -

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Basic information

Entry
Database: PDB / ID: 3hio
TitleCrystal structure of Ricin A-chain in complex with the cyclic tetranucleotide inhibitor, a transition state analogue
ComponentsRicin
KeywordsHydrolase/Hydrolase inhibitor / RTA / transition state / ribosome inactivating proteins / RIPs / Disulfide bond / Glycoprotein / Hydrolase / Lectin / Nucleotide-binding / Plant defense / Protein synthesis inhibitor / Toxin / Hydrolase-Hydrolase inhibitor COMPLEX
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHo, M. / Sturm, M.B. / Goldman, J.D. / Almo, S.C. / Schramm, V.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.
Authors: Ho, M.C. / Sturm, M.B. / Almo, S.C. / Schramm, V.L.
History
DepositionMay 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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

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Assembly

Deposited unit
A: Ricin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7623
Polymers30,0681
Non-polymers1,6942
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.632, 68.632, 134.681
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 / Ricin A chain / rRNA N-glycosidase


Mass: 30067.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical ChemComp-C2X / 9,9'-{(2R,3R,3aR,5S,7aR,9R,10R,10aR,12S,23R,25aR,27R,28R,28aR,30S,32aR,35aR,37S,39aR)-9-(6-amino-9H-purin-9-yl)-34-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-5,12,23,30,37-pentahydroxy-3,10,28-trimethoxy-5,12,23,30,37-pentaoxidotetracosahydro-2H,7H,25H-trifuro[3,2-f:3',2'-l:3'',2''-x]pyrrolo[3,4-r][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]undecaoxazapentaphosphacyclopentatriacontine-2,27-diyl}bis(2-amino-3,9-dihydro-6H-purin-6-one)


Mass: 1598.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H72N21O29P5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 25% PEG2000, 0.2M Lithium sulfate, 0.1M Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.081 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.081 Å / Relative weight: 1
ReflectionResolution: 2→61.2 Å / Num. obs: 22257 / % possible obs: 98.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.059 / Χ2: 1.013 / Net I/σ(I): 30.077
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.077.80.52321551.036197.6
2.07-2.158.30.37421791.023199.2
2.15-2.258.30.26221881.006199.8
2.25-2.378.30.17722161.023199.6
2.37-2.528.30.14322010.976199.9
2.52-2.718.30.09822121.014199.6
2.71-2.998.40.06722361.023199.7
2.99-3.428.40.04922620.963199.8
3.42-4.38.20.04622720.958199
4.3-207.90.03723361.11195.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.871 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1139 5.1 %RANDOM
Rwork0.219 ---
obs0.221 22185 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.27 Å2 / Biso mean: 21.98 Å2 / Biso min: 7.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--0.62 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 111 63 2216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222230
X-RAY DIFFRACTIONr_angle_refined_deg1.5572.0143062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0535266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07622.981104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32815329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.311521
X-RAY DIFFRACTIONr_chiral_restr0.0970.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211701
X-RAY DIFFRACTIONr_mcbond_it0.7781.51306
X-RAY DIFFRACTIONr_mcangle_it1.45522120
X-RAY DIFFRACTIONr_scbond_it2.5383924
X-RAY DIFFRACTIONr_scangle_it4.2214.5939
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 81 -
Rwork0.241 1487 -
all-1568 -
obs--96.61 %
Refinement TLS params.Method: refined / Origin x: -26.667 Å / Origin y: 14.935 Å / Origin z: 9.08 Å
111213212223313233
T0.2015 Å20.0252 Å2-0.0328 Å2-0.1611 Å20.0111 Å2--0.1809 Å2
L0.8906 °2-0.6686 °21.2494 °2-1.2484 °2-0.91 °2--2.6129 °2
S0.2109 Å °0.0029 Å °-0.1415 Å °-0.2133 Å °-0.0203 Å °0.1324 Å °0.3096 Å °0.0126 Å °-0.1906 Å °

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