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- PDB-1rgf: HYDROLASE, GUANYLORIBONUCLEASE -

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Basic information

Entry
Database: PDB / ID: 1rgf
TitleHYDROLASE, GUANYLORIBONUCLEASE
ComponentsRIBONUCLEASE
KeywordsHYDROLASE (GUANYLORIBONUCLEASE)
Function / homology
Function and homology information


ribonuclease T1 activity / ribonuclease T1 / RNA endonuclease activity / lyase activity / RNA binding / extracellular region
Similarity search - Function
Guanine-specific ribonuclease N1/T1/U2 / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / 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 1.3Nov 29, 2017Group: Advisory / Category: pdbx_unobs_or_zero_occ_atoms

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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
Water6,936385
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: (0.97236, 0.22911, 0.0451), (-0.04232, 0.36287, -0.93088), (-0.22964, 0.90324, 0.36253)
Vector: -33.29366, 21.1845, 18.72934)

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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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / 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.

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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 growpH: 6.7 / Details: ROOM TEMPERATURE, PH 6.7, AMMONIUM SULFATE / Temp details: room temp
Crystal grow
*PLUS
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 / σ(F): 0 /
Num. reflection% reflection
obs57561 95 %
Refine analyzeLuzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 0 385 1875
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.23
X-RAY DIFFRACTIONp_mcangle_it3.35
X-RAY DIFFRACTIONp_scbond_it6.56
X-RAY DIFFRACTIONp_scangle_it98
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.1490.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2750.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.270.3
X-RAY DIFFRACTIONp_planar_tor3.73
X-RAY DIFFRACTIONp_staggered_tor1515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor12.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS

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