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- PDB-1t2i: T76W mutant of RNase Sa from Streptomyces aureofaciens -

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Basic information

Entry
Database: PDB / ID: 1t2i
TitleT76W mutant of RNase Sa from Streptomyces aureofaciens
ComponentsGuanyl-specific ribonuclease Sa
KeywordsHYDROLASE / mutant / ribonuclease
Function / homology
Function and homology information


ribonuclease T1 / ribonuclease T1 activity / RNA endonuclease activity / lyase activity / RNA binding / extracellular region
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 Sa
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsUrbanikova, L. / Sevcik, J.
CitationJournal: Biophys.J. / Year: 2004
Title: Contribution of single tryptophan residues to the fluorescence and stability of ribonuclease sa.
Authors: Alston, R.W. / Urbanikova, L. / Sevcik, J. / Lasagna, M. / Reinhart, G.D. / Scholtz, J.M. / Pace, C.N.
History
DepositionApr 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
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
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanyl-specific ribonuclease Sa


Theoretical massNumber of molelcules
Total (without water)10,6681
Polymers10,6681
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.872, 40.462, 56.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Guanyl-specific ribonuclease Sa / RNase Sa


Mass: 10667.598 Da / Num. of mol.: 1 / Mutation: T76W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Strain: BMK / Gene: U39467 / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): NOVABLUE / References: UniProt: P05798, EC: 3.1.27.3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
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: 1.8 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: ammonium sulfate, disodium phosphate, monosodium phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.096 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2003
RadiationMonochromator: Si(111) channel-cut Xtal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.096 Å / Relative weight: 1
ReflectionResolution: 1.1→29 Å / Num. obs: 29254 / % possible obs: 95.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 53.3
Reflection shellResolution: 1.1→1.11 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 8.7 / Num. unique all: 705 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1rgg

1rgg


Resolution: 1.1→29 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.375 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16698 1560 5.1 %RANDOM
Rwork0.12839 ---
obs0.1303 29254 95.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.383 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.1→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 0 243 1070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021856
X-RAY DIFFRACTIONr_bond_other_d0.0020.02708
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.931177
X-RAY DIFFRACTIONr_angle_other_deg1.7331652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.775106
X-RAY DIFFRACTIONr_chiral_restr0.0840.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02990
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02190
X-RAY DIFFRACTIONr_nbd_refined0.2080.2171
X-RAY DIFFRACTIONr_nbd_other0.2460.2851
X-RAY DIFFRACTIONr_nbtor_other0.0860.2453
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.259
X-RAY DIFFRACTIONr_mcbond_it1.0031.5519
X-RAY DIFFRACTIONr_mcangle_it1.562847
X-RAY DIFFRACTIONr_scbond_it1.793337
X-RAY DIFFRACTIONr_scangle_it2.5434.5330
X-RAY DIFFRACTIONr_rigid_bond_restr0.9252856
X-RAY DIFFRACTIONr_sphericity_free2.8552243
X-RAY DIFFRACTIONr_sphericity_bonded2.2712828
LS refinement shellResolution: 1.1→1.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.168 106 -
Rwork0.165 2030 -
obs-705 90.2 %

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