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- PDB-1jbr: Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD ... -

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Basic information

Entry
Database: PDB / ID: 1jbr
TitleCrystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor
Components
  • 31-mer SRD RNA analog
  • 5'-R(*GP*CP*GP*CP*UP*CP*CP*UP*CP*AP*GP*UP*AP*CP*GP*AP*GP*(A23))-3'
  • 5'-R(*GP*GP*AP*AP*CP*CP*GP*GP*AP*GP*CP*GP*C)-3'
  • Restrictocin
KeywordsHYDROLASE/RNA / protein-RNA interaction / specific recognition / restrictocin / ribosomal RNA / sarcin/ricin domain / base flipping / HYDROLASE-RNA COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / negative regulation of translation / RNA binding / extracellular region
Similarity search - Function
Fungal ribotoxin / : / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Ribonuclease mitogillin
Similarity search - Component
Biological speciesAspergillus restrictus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsYang, X. / Gerczei, T. / Glover, L. / Correll, C.C.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping.
Authors: Yang, X. / Gerczei, T. / Glover, L.T. / Correll, C.C.
History
DepositionJun 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
C: 5'-R(*GP*CP*GP*CP*UP*CP*CP*UP*CP*AP*GP*UP*AP*CP*GP*AP*GP*(A23))-3'
F: 5'-R(*GP*GP*AP*AP*CP*CP*GP*GP*AP*GP*CP*GP*C)-3'
D: 31-mer SRD RNA analog
A: Restrictocin
B: Restrictocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,04610
Polymers53,8515
Non-polymers1955
Water3,027168
1
C: 5'-R(*GP*CP*GP*CP*UP*CP*CP*UP*CP*AP*GP*UP*AP*CP*GP*AP*GP*(A23))-3'
F: 5'-R(*GP*GP*AP*AP*CP*CP*GP*GP*AP*GP*CP*GP*C)-3'
A: Restrictocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0125
Polymers26,9343
Non-polymers782
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 31-mer SRD RNA analog
B: Restrictocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0345
Polymers26,9172
Non-polymers1173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.4, 109.7, 40.0
Angle α, β, γ (deg.)90.0, 97.8, 90.0
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 3 types, 3 molecules CFD

#1: RNA chain 5'-R(*GP*CP*GP*CP*UP*CP*CP*UP*CP*AP*GP*UP*AP*CP*GP*AP*GP*(A23))-3'


Mass: 5809.448 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(*GP*GP*AP*AP*CP*CP*GP*GP*AP*GP*CP*GP*C)-3'


Mass: 4234.621 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: RNA chain 31-mer SRD RNA analog


Mass: 10027.062 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence contains 14 highly conserved nucleotides among all living species.

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Protein , 1 types, 2 molecules AB

#4: Protein Restrictocin / ribonuclease mitogillin


Mass: 16889.877 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aspergillus restrictus (mold)
References: UniProt: P67876, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

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Non-polymers , 2 types, 173 molecules

#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG5000, K-MES, KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG500011
2K-MES11
3KCl11
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris1drop
250 mM1dropKCl
350 mMsodium-EDTA1drop
42-10 %(w/v)PEG5000 MME1reservoir
5100 mMpotassium-MES1reservoir
650 mM1reservoirKCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 22, 2000 / Details: mirrors
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→500 Å / Num. all: 28101 / Num. obs: 24648 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.66 % / Biso Wilson estimate: 51.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.2
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 2.16 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.37 / Num. unique all: 1277 / % possible all: 92.4
Reflection
*PLUS
Lowest resolution: 500 Å
Reflection shell
*PLUS
% possible obs: 92.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1aqz

1aqz


Resolution: 2.15→19.96 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS parameter file
Details: Electron density around A17 in chain C indicates a mixture of multiple conformations. Only the cleaved conformation has been modeled, and some water molecules around A17 in chain C may ...Details: Electron density around A17 in chain C indicates a mixture of multiple conformations. Only the cleaved conformation has been modeled, and some water molecules around A17 in chain C may represent the alternative conformation(s) of A17.
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2437 9.9 %random
Rwork0.232 ---
all0.238 28101 --
obs0.238 24648 88.4 %-
Solvent computationSolvent model: flat model / Bsol: 40.7006 Å2 / ksol: 0.318052 e/Å3
Displacement parametersBiso mean: 50.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å213.9 Å2
2---3.96 Å20 Å2
3---3.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.15→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 1328 5 168 3883
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006381
X-RAY DIFFRACTIONc_angle_deg1.29824
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.572
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.426 337 10.5 %
Rwork0.417 2879 -
obs--69.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-ALLATOM.PARAMDNA-RNA-ALLATOM.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.232 / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.426 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.417

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