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- PDB-5gu4: rRNA N-glycosylase RTA -

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Basic information

Entry
Database: PDB / ID: 5gu4
TitlerRNA N-glycosylase RTA
Components
  • GLY-PHE-GLY-LEU-PHE-ASP
  • Ricin
KeywordsHYDROLASE / Ricin / ribosome-inactivating protein / ribosomal P stalk protein / ribosome
Function / homology
Function and homology information


cytoplasmic translational elongation / rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane ...cytoplasmic translational elongation / rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / defense response / Regulation of expression of SLITs and ROBOs / toxin activity / carbohydrate binding / killing of cells of another organism / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / structural constituent of ribosome / translation / focal adhesion / extracellular exosome / membrane / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / 60s Acidic ribosomal protein / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. ...Ribosomal protein P2 / Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / 60s Acidic ribosomal protein / 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
Ricin / Large ribosomal subunit protein P2
Similarity search - Component
Biological speciesRicinus communis (castor bean)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsShi, W.W. / Tang, Y.S. / Sze, S.Y. / Zhu, Z.N. / Wong, K.B. / Shaw, P.C.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The Chinese University of Hong KongProject Ref. No. C4045-14G Hong Kong
CitationJournal: Toxins / Year: 2016
Title: Crystal Structure of Ribosome-Inactivating Protein Ricin A Chain in Complex with the C-Terminal Peptide of the Ribosomal Stalk Protein P2
Authors: Shi, W.W. / Tang, Y.S. / Sze, S.Y. / Zhu, Z.N. / Wong, K.B. / Shaw, P.C.
History
DepositionAug 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin
B: Ricin
C: GLY-PHE-GLY-LEU-PHE-ASP
D: GLY-PHE-GLY-LEU-PHE-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1045
Polymers69,0124
Non-polymers921
Water3,837213
1
A: Ricin
C: GLY-PHE-GLY-LEU-PHE-ASP


Theoretical massNumber of molelcules
Total (without water)34,5062
Polymers34,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-8 kcal/mol
Surface area11450 Å2
MethodPISA
2
B: Ricin
D: GLY-PHE-GLY-LEU-PHE-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5983
Polymers34,5062
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-8 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.450, 59.880, 67.495
Angle α, β, γ (deg.)90.000, 99.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ricin


Mass: 33489.691 Da / Num. of mol.: 2 / 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: Protein/peptide GLY-PHE-GLY-LEU-PHE-ASP


Mass: 1016.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05387*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1.95 Å3/Da / Density % sol: 36.78 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2.8 M sodium acetate, tetrahydrate pH7.0 30%-35% glucose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→25 Å / Num. obs: 75182 / % possible obs: 97.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Χ2: 1.044 / Net I/av σ(I): 23.978 / Net I/σ(I): 17.2 / Num. measured all: 272881
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.613.60.33973780.8940.2050.3970.81696.4
1.61-1.673.70.24674450.9420.1480.2880.88897.5
1.67-1.753.70.17674200.9690.1060.2050.97197.6
1.75-1.843.70.12475470.9830.0740.1441.16997.9
1.84-1.953.70.08875150.990.0530.1031.25498.2
1.95-2.13.70.06375220.9940.0380.0741.24498.1
2.1-2.313.70.05175500.9960.0310.0591.05798.3
2.31-2.653.60.04675850.9960.0280.0541.00198.5
2.65-3.343.50.04176480.9970.0260.0490.99598.7
3.34-253.40.03575720.9970.0220.0421.01996.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PX8

3px8


Resolution: 1.55→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.751 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 3754 5 %RANDOM
Rwork0.2176 ---
obs0.2195 71323 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.28 Å2 / Biso mean: 20.373 Å2 / Biso min: 9.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0.18 Å2
2--0.03 Å20 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 1.55→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 6 213 4333
Biso mean--28.89 26.79 -
Num. residues----522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0224208
X-RAY DIFFRACTIONr_angle_refined_deg2.1851.9475718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8175519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64522.925212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90815652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8471542
X-RAY DIFFRACTIONr_chiral_restr0.1490.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213278
X-RAY DIFFRACTIONr_mcbond_it1.611.52595
X-RAY DIFFRACTIONr_mcangle_it2.524179
X-RAY DIFFRACTIONr_scbond_it3.66431613
X-RAY DIFFRACTIONr_scangle_it5.6644.51539
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 260 -
Rwork0.361 5128 -
all-5388 -
obs--95.13 %

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