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- PDB-1tto: Crystal structure of the Rnase T1 variant R2 -

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Basic information

Entry
Database: PDB / ID: 1tto
TitleCrystal structure of the Rnase T1 variant R2
ComponentsRNase T1
KeywordsHYDROLASE / ribonuclease / adenine specificity
Function / homology
Function and homology information


hyphal tip / ribonuclease T1 / ribonuclease T1 activity / cell septum / RNA endonuclease activity / lyase activity / RNA binding
Similarity search - Function
: / : / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHahn, U. / Czaja, R. / Perbandt, M. / Betzel, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2005
Title: Purine activity of RNase T1RV is further improved by substitution of Trp59 by tyrosine
Authors: Czaja, R. / Perbandt, M. / Betzel, C. / Hahn, U.
History
DepositionJun 23, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNase T1
B: RNase T1
C: RNase T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6876
Polymers33,3203
Non-polymers3663
Water6,125340
1
A: RNase T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2292
Polymers11,1071
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNase T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2292
Polymers11,1071
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNase T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2292
Polymers11,1071
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.524, 56.524, 159.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein RNase T1


Mass: 11106.709 Da / Num. of mol.: 3 / Mutation: k41e, y42f, n43r, y45w, e46n, w59y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Plasmid: pA2T1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00651, EC: 3.1.27.3
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.2 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, tris-Cl, calcium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13
DetectorDate: Apr 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→50 Å / Biso Wilson estimate: 13.3 Å2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q9E

1q9e


Resolution: 2.1→48.95 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1817657.65 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 842 5 %RANDOM
Rwork0.187 ---
obs-16730 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.0963 Å2 / ksol: 0.343661 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å21.94 Å20 Å2
2--2.66 Å20 Å2
3----5.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 24 340 2710
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_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it2.121.5
X-RAY DIFFRACTIONc_mcangle_it2.82
X-RAY DIFFRACTIONc_scbond_it3.372
X-RAY DIFFRACTIONc_scangle_it4.142.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 149 5.4 %
Rwork0.233 2620 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3tmn_xplor_par.txttmn_xplor_top.txt

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