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- PDB-1jbs: Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA ... -

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Basic information

Entry
Database: PDB / ID: 1jbs
TitleCrystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog
Components
  • 29-mer sarcin/ricin domain RNA analog
  • restrictocin
KeywordsHYDROLASE/RNA / ribotoxin / highly specific ribonuclease / protein-RNA complex / ribonuclease T1 / HYDROLASE-RNA COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / negative regulation of translation / RNA binding / extracellular region
Similarity search - Function
Fungal ribotoxin / : / Guanine-specific ribonuclease N1/T1/U2 / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Ribonuclease mitogillin / Ribonuclease mitogillin
Similarity search - Component
Biological speciesAspergillus restrictus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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: Non-polymer description / Version format compliance
Revision 1.3May 29, 2013Group: Atomic model
Revision 1.4Aug 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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: 29-mer sarcin/ricin domain RNA analog
D: 29-mer sarcin/ricin domain RNA analog
A: restrictocin
B: restrictocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,02610
Polymers52,7924
Non-polymers2356
Water6,143341
1
C: 29-mer sarcin/ricin domain RNA analog
A: restrictocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5135
Polymers26,3962
Non-polymers1173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 29-mer sarcin/ricin domain RNA analog
B: restrictocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5135
Polymers26,3962
Non-polymers1173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.511, 101.863, 41.092
Angle α, β, γ (deg.)90.00, 92.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain 29-mer sarcin/ricin domain RNA analog


Mass: 9505.949 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The sequence contains 14 highly conserved nucleotides among all living species.
#2: 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: P04389, UniProt: P67876*PLUS, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#3: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.47 Å3/Da / Density % sol: 50.28 %
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: May 27, 2000 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→19.8 Å / Num. all: 36306 / Num. obs: 36294 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.24 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 26.3
Reflection shellResolution: 1.97→2 Å / Redundancy: 4.44 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.48 / % possible all: 98.9
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 98.9 %

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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: 1.97→19.8 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: CNS topology and parameter files
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 2532 7.5 %random
Rwork0.213 ---
all0.217 36306 --
obs0.217 33893 93.4 %-
Solvent computationSolvent model: flat model / Bsol: 40.4043 Å2 / ksol: 0.353848 e/Å3
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å20 Å2-11.19 Å2
2---1.03 Å20 Å2
3----1.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.97→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 1258 6 341 3987
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it1.532
X-RAY DIFFRACTIONc_scangle_it2.192.5
LS refinement shellResolution: 1.97→2.09 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 382 7.3 %
Rwork0.313 4875 -
obs--87.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2RNA-METHYL.PARAMRNA-METHYL.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 19.8 Å / σ(F): 0 / % reflection Rfree: 7.5 % / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
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: 0.334 / % reflection Rfree: 7.3 % / Rfactor Rwork: 0.313

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