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- PDB-1t2h: Y81W mutant of RNase Sa from Streptomyces aureofaciens -

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Basic information

Entry
Database: PDB / ID: 1t2h
TitleY81W 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 Å
AuthorsSevcik, J. / Urbanikova, L.
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 / 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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
B: Guanyl-specific ribonuclease Sa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3073
Polymers21,2112
Non-polymers961
Water10,611589
1
A: Guanyl-specific ribonuclease Sa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7022
Polymers10,6061
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanyl-specific ribonuclease Sa


Theoretical massNumber of molelcules
Total (without water)10,6061
Polymers10,6061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.206, 64.309, 77.666
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: 10605.527 Da / Num. of mol.: 2 / Mutation: Y81W
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: ammonium sulfate, disodium phosphate, monosodium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.812 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2003
RadiationMonochromator: Si(111) double monochromator system / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 1→33.3 Å / Num. obs: 103514 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 34.5
Reflection shellResolution: 1→1.01 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 10.2 / Num. unique all: 4121 / % possible all: 97.7

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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→33 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.31 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16593 5166 5 %RANDOM
Rwork0.14524 ---
obs0.14631 98348 99.56 %-
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: 8.056 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 5 589 2280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211739
X-RAY DIFFRACTIONr_bond_other_d0.0030.021448
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9392386
X-RAY DIFFRACTIONr_angle_other_deg0.87433374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0785214
X-RAY DIFFRACTIONr_chiral_restr0.0910.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021998
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02372
X-RAY DIFFRACTIONr_nbd_refined0.2330.2393
X-RAY DIFFRACTIONr_nbd_other0.2630.21775
X-RAY DIFFRACTIONr_nbtor_other0.0830.2918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2471
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.293
X-RAY DIFFRACTIONr_mcbond_it1.1791.51068
X-RAY DIFFRACTIONr_mcangle_it1.80421743
X-RAY DIFFRACTIONr_scbond_it2.0683671
X-RAY DIFFRACTIONr_scangle_it2.9124.5643
X-RAY DIFFRACTIONr_rigid_bond_restr0.93221739
X-RAY DIFFRACTIONr_sphericity_free5.7665589
X-RAY DIFFRACTIONr_sphericity_bonded4.16651691
LS refinement shellResolution: 1→1.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.178 367 -
Rwork0.166 7157 -
obs-4121 97.7 %

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