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- PDB-1jbt: CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-M... -

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Basic information

Entry
Database: PDB / ID: 1jbt
TitleCRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG
Components
  • 29-MER SARCIN/RICIN DOMAIN RNA ANALOG
  • RESTRICTOCIN
KeywordsHYDROLASE/RNA / restrictocin / ribotoxin / highly specific ribonuclease / ribonuclease T1 / protein-RNA recognition / 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 / : / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / 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: 2.7 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)52,76810
Polymers52,5334
Non-polymers2356
Water00
1
C: 29-MER SARCIN/RICIN DOMAIN RNA ANALOG
A: RESTRICTOCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3845
Polymers26,2672
Non-polymers1173
Water0
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)26,3845
Polymers26,2672
Non-polymers1173
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.001, 102.822, 41.617
Angle α, β, γ (deg.)90.00, 93.88, 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: 9376.675 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The RNA 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: P67876, 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
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.16 %
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, 2001 / 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: 2.7→500 Å / Num. all: 14550 / Num. obs: 14201 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 47.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.2
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.8 / % possible all: 96.5
Reflection shell
*PLUS
% possible obs: 96.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AQZ

1aqz


Resolution: 2.7→19.77 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: CNS_solve 1.0 topology and parameter files
RfactorNum. reflection% reflectionSelection details
Rfree0.282 982 7.5 %random
Rwork0.2238 ---
all0.229 14363 --
obs0.229 13019 90.9 %-
Solvent computationSolvent model: flat model / Bsol: 21.8659 Å2 / ksol: 0.296617 e/Å3
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å20 Å2-20.02 Å2
2---16.77 Å20 Å2
3---14.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 1242 6 0 3630
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_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it2.461.5
X-RAY DIFFRACTIONc_mcangle_it4.082
X-RAY DIFFRACTIONc_scbond_it3.112
X-RAY DIFFRACTIONc_scangle_it4.432.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 148 7.9 %
Rwork0.389 1720 -
obs--78.6 %
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: 7.5 % / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
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: 0.417 / % reflection Rfree: 7.9 % / Rfactor Rwork: 0.389

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