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- PDB-1py3: Crystal structure of Ribonuclease Sa2 -

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Basic information

Entry
Database: PDB / ID: 1py3
TitleCrystal structure of Ribonuclease Sa2
Componentsribonuclease
KeywordsHYDROLASE / ALPHA-BETA STRUCTURE
Function / homology
Function and homology information


: / RNA endonuclease 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 8, 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 1.3Jul 25, 2012Group: Other
Revision 1.4Aug 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: ribonuclease
B: ribonuclease
C: ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8234
Polymers32,7273
Non-polymers961
Water4,990277
1
A: ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0052
Polymers10,9091
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ribonuclease


Theoretical massNumber of molelcules
Total (without water)10,9091
Polymers10,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ribonuclease


Theoretical massNumber of molelcules
Total (without water)10,9091
Polymers10,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.290, 68.700, 57.510
Angle α, β, γ (deg.)90.00, 100.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-27-

ASN

21A-317-

HOH

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Components

#1: Protein ribonuclease


Mass: 10909.012 Da / Num. of mol.: 3
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.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 3.03 Å3/Da / Density % sol: 59.46 %
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: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9185 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 17, 1996 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9185 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. all: 35955 / Num. obs: 35955 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.96 / Num. unique all: 1759 / % possible all: 98.4

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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: 1.8→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.443 / SU ML: 0.077 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.149 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21825 1796 5 %RANDOM
Rwork0.17246 ---
all0.175 ---
obs0.17484 34158 99.2 %-
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: 26.486 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20.13 Å2
2--2.17 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 5 277 2497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0212313
X-RAY DIFFRACTIONr_bond_other_d0.0020.021987
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9463143
X-RAY DIFFRACTIONr_angle_other_deg2.11234630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2825274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1230.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022617
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02504
X-RAY DIFFRACTIONr_nbd_refined0.240.2454
X-RAY DIFFRACTIONr_nbd_other0.2540.22328
X-RAY DIFFRACTIONr_nbtor_other0.0980.21422
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.0481.51386
X-RAY DIFFRACTIONr_mcangle_it3.22922243
X-RAY DIFFRACTIONr_scbond_it4.1793927
X-RAY DIFFRACTIONr_scangle_it6.3324.5900
X-RAY DIFFRACTIONr_rigid_bond_restr2.13122313
X-RAY DIFFRACTIONr_sphericity_free16.6165277
X-RAY DIFFRACTIONr_sphericity_bonded5.69352251
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.28 119
Rwork0.203 2426
obs-2426

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