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- PDB-1rgh: HYDROLASE, GUANYLORIBONUCLEASE -

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Basic information

Entry
Database: PDB / ID: 1rgh
TitleHYDROLASE, GUANYLORIBONUCLEASE
ComponentsRIBONUCLEASE
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
Guanyl-specific ribonuclease Sa
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsSevcik, J. / Dauter, Z. / Lamzin, V.S. / Wilson, K.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Ribonuclease from Streptomyces aureofaciens at atomic resolution.
Authors: Sevcik, J. / Dauter, Z. / Lamzin, V.S. / Wilson, K.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Complex of Ribonuclease from Streptomyces Aureofaciens with 2'-Gmp at 1.7A Resolution
Authors: Sevcik, J. / Hill, C.P. / Dauter, Z. / Wilson, K.S.
#2: 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.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Determination and Restrained Least-Squares Refinement of the Structures of Ribonuclease Sa and its Complex with 3'-Guanylic Acid at 1.8 A Resolution
Authors: Sevcik, J. / Dodson, E.J. / Dodson, G.G.
#4: 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.
#5: Journal: FEBS Lett. / Year: 1986
Title: Amino Acid Sequence Determination of Guanyl-Specific Ribonuclease Sa from Streptomyces Aureofaciens
Authors: Shlyapnikov, S.V. / Both, V. / Kulikov, V.A. / Dementiev, A.A. / Sevcik, J. / Zelinka, J.
#6: Journal: Biochim.Biophys.Acta / Year: 1971
Title: Exocellular Ribonuclease from Streptomyces Aureofaciens. I. Isolation and Purification
Authors: Bacova, M. / Zelinkova, E. / Zelinka, J.
#7: Journal: Biochim.Biophys.Acta / Year: 1971
Title: Exocellular Ribonuclease from Streptomyces Aureofaciens. II. Properties and Specificity
Authors: Zelinkova, E. / Bacova, M. / Zelinka, J.
History
DepositionJun 5, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...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_entry_details / pdbx_modification_feature / 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
B: RIBONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3574
Polymers21,1652
Non-polymers1922
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.820, 78.560, 39.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.97224, 0.22967, 0.04478), (-0.04292, 0.36316, -0.93074), (-0.23003, 0.90298, 0.36293)
Vector: -33.28425, 21.22728, 18.74696)

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Components

#1: Protein RIBONUCLEASE


Mass: 10582.492 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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURE BOUNDARIES HAVE BEEN DETERMINED USING SS PROGRAM (V.S.LAMZIN, EMBL HAMBURG) AS ...SECONDARY STRUCTURE BOUNDARIES HAVE BEEN DETERMINED USING 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: 47.6 %
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.0 %protein1drop
20.1 Mphosphate1drop
322 %satammonium sulfate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionRedundancy: 4.1 % / Rmerge(I) obs: 0.039
Reflection
*PLUS
Highest resolution: 1.2 Å / Num. obs: 60670 / % possible obs: 95.3 % / Num. measured all: 246637 / Biso Wilson estimate: 10.8 Å2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-93model building
SHELXL-93refinement
SHELXL-93phasing
RefinementResolution: 1.2→10 Å / Num. parameters: 7268 / Num. restraintsaints: 6152 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOU VALUES HAVE BEEN SUPPLIED FOR GLU B 54. THEY HAVE GENERATED FOR THE REMAINING ATOMS FROM THE B VALUES.
RfactorNum. reflection% reflection
all0.173 59491 -
obs--95 %
Solvent computationSolvent model: BASED ON BABINET'S PRINCIPLE
Refine analyzeNum. disordered residues: 5 / Occupancy sum non hydrogen: 1794
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 0 292 1782
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.229
X-RAY DIFFRACTIONs_zero_chiral_vol0.102
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.138
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.1
X-RAY DIFFRACTIONs_similar_adp_cmpnt2.5
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONs_plane_restr0.2290.274
X-RAY DIFFRACTIONs_chiral_restr0.1020.2

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