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- PDB-1pyl: Crystal structure of Ribonuclease Sa2 -

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Basic information

Entry
Database: PDB / ID: 1pyl
TitleCrystal structure of Ribonuclease Sa2
Componentsribonuclease
KeywordsHYDROLASE / ALPHA-BETA STRUCTURE
Function / homology
Function and homology information


: / RNA endonuclease activity / hydrolase 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
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.507 Å
AuthorsSevcik, J. / Dauter, Z. / Wilson, K.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystal structure reveals two alternative conformations in the active site of ribonuclease Sa2.
Authors: Sevcik, J. / Dauter, Z. / Wilson, K.S.
#1: Journal: Protein Expr.Purif. / Year: 1997
Title: Purification of Ribonucleases Sa, Sa2 and Sa3 after Expression in Escherichia coli
Authors: Hebert, E.J. / Grimsley, G.R. / Hartley, R.W. / Horn, G. / Schell, D. / Garcia, S. / Both, V. / Sevcik, J. / Pace, C.N.
History
DepositionJul 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: ribonuclease
B: ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2026
Polymers21,8182
Non-polymers3844
Water3,081171
1
A: ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1013
Polymers10,9091
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1013
Polymers10,9091
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.980, 34.130, 72.270
Angle α, β, γ (deg.)90.00, 109.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ribonuclease


Mass: 10909.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Strain: R8-26 / Plasmid: pEH100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53752, EC: 3.1.4.8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 45.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: ammonium sulfate, phosphate buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 30, 1997 / Details: MIRRORS
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. all: 30643 / Num. obs: 30643 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 22.3
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.65 / Num. unique all: 1894 / % 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: 1.507→25 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.165 / SU ML: 0.043 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.081 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1723 975 3.2 %RANDOM
Rwork0.14933 ---
all0.15 ---
obs0.15009 29668 98.14 %-
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: 22.179 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å2-0.44 Å2
2--0.9 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.507→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 20 171 3215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211613
X-RAY DIFFRACTIONr_bond_other_d0.0020.021355
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9522191
X-RAY DIFFRACTIONr_angle_other_deg1.74533162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4645190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021816
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02347
X-RAY DIFFRACTIONr_nbd_refined0.2990.2422
X-RAY DIFFRACTIONr_nbd_other0.2570.21589
X-RAY DIFFRACTIONr_nbtor_other0.1340.21181
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.6131.5963
X-RAY DIFFRACTIONr_mcangle_it2.65321553
X-RAY DIFFRACTIONr_scbond_it3.5073650
X-RAY DIFFRACTIONr_scangle_it5.1784.5638
X-RAY DIFFRACTIONr_rigid_bond_restr1.5821613
X-RAY DIFFRACTIONr_sphericity_free10.9825171
X-RAY DIFFRACTIONr_sphericity_bonded4.63951576
LS refinement shellResolution: 1.507→1.546 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 69 -
Rwork0.247 1894 -
obs-1894 90.2 %

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