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- PDB-1rsn: RIBONUCLEASE (RNASE SA) (E.C.3.1.4.8) COMPLEXED WITH EXO-2',3'-CY... -

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Basic information

Entry
Database: PDB / ID: 1rsn
TitleRIBONUCLEASE (RNASE SA) (E.C.3.1.4.8) COMPLEXED WITH EXO-2',3'-CYCLOPHOSPHOROTHIOATE
ComponentsRIBONUCLEASE SA
KeywordsHYDROLASE (GUANYLORIBONUCLEASE)
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
GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE / Guanyl-specific ribonuclease Sa
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSevcik, J. / Dauter, Z. / Lamzin, V.S. / Wilson, K.S.
Citation
Journal: Eur.J.Biochem. / Year: 1993
Title: Complex of ribonuclease Sa with a cyclic nucleotide and a proposed model for the reaction intermediate.
Authors: Sevcik, J. / Zegers, I. / Wyns, L. / Dauter, Z. / Wilson, K.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Complex of Ribonuclease from Streptomyces Aureofaciens with 2'-Gmp at 1.7 Angstroms Resolution
Authors: Sevcik, J. / Hill, C.P. / Dauter, Z. / Wilson, K.S.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Determination and Restrained Least-Squares Refinement of the Structure of Ribonuclease And its Complex with 3'-Guanylic Acid at 1.8 Angstroms Resolution
Authors: Sevcik, J. / Dodson, E.J. / Dodson, G.G.
#3: Journal: Trends Biochem.Sci. / Year: 1990
Title: Comparison of Active Sites of Some Microbial Ribonucleases: Structural Basis for Guanylic Specificity
Authors: Sevcik, J. / Sanishvili, R.G. / Pavlovsky, A.G. / Polyakov, K.M.
#4: Journal: FEBS Lett. / Year: 1986
Title: Amino Acid Sequence Determination of Guanyl-Specific Ribonuclease Sa from Streptomyces Aureofaciens
Authors: Shlyapnikov, S.U. / Both, V. / Kulikov, V.A. / Dementiev, A.A. / Sevcik, J. / Zelinka, J.
#5: Journal: Biochim.Biophys.Acta / Year: 1971
Title: Exocellular Ribonuclease from Streptomyces Aureofaciens. I. Isolation and Purification
Authors: Bacova, M. / Zelinkova, E. / Zelinka, J.
#6: Journal: Biochim.Biophys.Acta / Year: 1971
Title: Exocellular Ribonuclease from Streptomyces Aureofaciens. II. Properties and Specificity
Authors: Bacova, M. / Zelinkova, E. / Zelinka, J.
History
DepositionSep 1, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type / 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 / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE SA
B: RIBONUCLEASE SA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9885
Polymers21,1692
Non-polymers8193
Water8,125451
1
A: RIBONUCLEASE SA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0423
Polymers10,5851
Non-polymers4572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIBONUCLEASE SA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9462
Polymers10,5851
Non-polymers3611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.700, 78.800, 39.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 27 / 2: CIS PROLINE - PRO B 27
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.96983, 0.24082, 0.03791), (-0.05449, 0.36571, -0.92913), (-0.23761, 0.89903, 0.3678)
Vector: -33.14381, 21.88471, 19.1442)
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO CHEMICALLY IDENTICAL SUBUNITS WHICH ARE RELATED BY A NON-CRYSTALLOGRAPHIC SYMMETRY. MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 1 .. A 96 B 1 .. B 96 0.375

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Components

#1: Protein RIBONUCLEASE SA


Mass: 10584.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces aureofaciens (bacteria) / 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: Chemical ChemComp-SGP / GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE


Mass: 361.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURE BOUNDARIES HAVE BEEN DETERMINED USING THE SS PROGRAM (V.S.LAMZIN, EMBL HAMBURG) ...SECONDARY STRUCTURE BOUNDARIES HAVE BEEN DETERMINED USING THE SS PROGRAM (V.S.LAMZIN, EMBL HAMBURG) AS DESCRIBED IN V.S.LAMZIN,Z.DAUTER,V.O.POPOV,E.H.HARUTYUNYAN,K.S.WILSON J.MOL.BIOL. (1994) V.236, 759-785.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 %protein 1drop
20.1 Msodium phosphate1drop
3ammonium sulfate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Rmerge(I) obs: 0.034
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 13932 / % possible obs: 98.4 % / Num. measured all: 48382 / Rmerge(I) obs: 0.034

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PROLSQrefinement
RefinementResolution: 2→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.119 13889
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 51 451 1995
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0470.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0780.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.92
X-RAY DIFFRACTIONp_mcangle_it3.83
X-RAY DIFFRACTIONp_scbond_it5.94
X-RAY DIFFRACTIONp_scangle_it7.35
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.1720.15
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_multtor_nbd0.2620.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2150.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.13
X-RAY DIFFRACTIONp_staggered_tor13.715
X-RAY DIFFRACTIONp_orthonormal_tor13.820
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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