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- PDB-1ucl: Mutants of RNase Sa -

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Basic information

Entry
Database: PDB / ID: 1ucl
TitleMutants of RNase Sa
ComponentsGuanyl-specific ribonuclease Sa
KeywordsHYDROLASE / Protein Stability / Hydrogen Bond / Burial Polar
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 / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsTakano, K. / Scholtz, J.M. / Sacchettini, J.C. / Pace, C.N.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The contribution of polar group burial to protein stability is strongly context-dependent
Authors: Takano, K. / Scholtz, J.M. / Sacchettini, J.C. / Pace, C.N.
History
DepositionApr 15, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Nov 13, 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)21,2653
Polymers21,1692
Non-polymers961
Water4,936274
1
A: Guanyl-specific ribonuclease Sa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6812
Polymers10,5841
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanyl-specific ribonuclease Sa


Theoretical massNumber of molelcules
Total (without water)10,5841
Polymers10,5841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.261, 77.658, 38.344
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: 10584.466 Da / Num. of mol.: 2 / Mutation: V57T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Plasmid: pEH100 / Production host: Escherichia coli (E. coli) / 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.: 274 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 2.0M ammonium sulfate, 0.1M HEPES-Na pH 7.5, 2%(v/v) PEG400, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MTris1droppH8.4
210 mg/mlprotein1drop
32.0 Mammonium sulfate1reservoir
40.1 Msodium HEPES1reservoirpH7.5
52 %(v/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.82 Å / Num. all: 17544 / Num. obs: 17301 / % possible obs: 99.3 % / Biso Wilson estimate: 5.8 Å2
Reflection
*PLUS
Num. obs: 17544 / Num. measured all: 98889 / Rmerge(I) obs: 0.062

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→14.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 295717.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1708 9.9 %RANDOM
Rwork0.176 ---
obs0.176 17252 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.6153 Å2 / ksol: 0.441062 e/Å3
Displacement parametersBiso mean: 12.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å20 Å2
2--1.85 Å20 Å2
3---0.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.82→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 5 274 1771
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it2.632
X-RAY DIFFRACTIONc_scangle_it4.032.5
LS refinement shellResolution: 1.82→1.93 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 225 8.9 %
Rwork0.216 2299 -
obs--86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69

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