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- PDB-1rnt: RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF T... -

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Entry
Database: PDB / ID: 1rnt
TitleRESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF THE RIBONUCLEASE T1(ASTERISK)2(PRIME)-GUANYLIC ACID COMPLEX AT 1.9 ANGSTROMS RESOLUTION
ComponentsRIBONUCLEASE T1 ISOZYME
KeywordsHYDROLASE(ENDORIBONUCLEASE)
Function / homology
Function and homology information


hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / endonuclease activity / lyase activity / RNA binding
Similarity search - Function
: / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-2'-MONOPHOSPHATE / Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsSaenger, W. / Arni, R. / Heinemann, U. / Tokuoka, R.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1987
Title: Restrained Least-Squares Refinement of the Crystal Structure of the Ribonuclease T1(Asterisk)2(Prime)-Guanylic Acid Complex at 1.9 Angstroms Resolution
Authors: Arni, R. / Heinemann, U. / Maslowska, M. / Tokuoka, R. / Saenger, W.
#1: Journal: J.Biol.Chem. / Year: 1988
Title: Three-Dimensional Structure of the Ribonuclease T1(Asterisk)2(Prime)-Gmp Complex at 1.9-Angstroms Resolution
Authors: Arni, R. / Heinemann, U. / Tokuoka, R. / Saenger, W.
#2: Journal: Fresenius Z.Anal.Chem. / Year: 1987
Title: Struktur Und Funktion Des Enzyms Ribonuclease T1 (German)
Authors: Arni, R. / Heinemann, U. / Saenger, W.
#3: Journal: Pure Appl.Chem. / Year: 1985
Title: Mechanism of Guanosine Recognition and RNA Hydrolysis by Ribonuclease T1
Authors: Heinemann, U. / Saenger, W.
#4: Journal: Trends Biochem.Sci.(Pers. Ed.) / Year: 1983
Title: The Structural and Sequence Homology of a Family of Microbial Ribonucleases
Authors: Hill, C. / Dodson, G. / Heinemann, U. / Saenger, W. / Mitsui, Y. / Nakamura, K. / Borisov, S. / Tischenko, G. / Polyakov, K. / Pavlovsky, S.
#5: Journal: Jerusalem Symp.Quantum Chem.Biochem. / Year: 1983
Title: Ribonuclease T1. Mechanism of Specific Guanine Recognition and RNA Hydrolysis
Authors: Heinemann, U. / Saenger, W.
#6: Journal: J.Biomol.Struct.Dyn. / Year: 1983
Title: Crystallographic Study of Mechanism of Ribonuclease T1-Catalysed Specific RNA Hydrolysis
Authors: Heinemann, U. / Saenger, W.
#7: Journal: Nature / Year: 1982
Title: Specific Protein-Nucleic Acid Recognition in Ribonuclease T1-2(Prime)-Guanylic Acid Complex. An X-Ray Study
Authors: Heinemann, U. / Saenger, W.
#8: Journal: Eur.J.Biochem. / Year: 1980
Title: Crystallization of a Complex between Ribonuclease T1 and 2(Prime)-Guanylic Acid
Authors: Heinemann, U. / Wernitz, M. / Paehler, A. / Saenger, W. / Menke, G. / Rueterjans, H.
History
DepositionJul 10, 1987Processing site: BNL
Revision 1.0Oct 16, 1987Provider: 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: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE T1 ISOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4582
Polymers11,0951
Non-polymers3631
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.810, 50.110, 40.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES 39 AND 55 ARE CIS-PROLINES.

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Components

#1: Protein RIBONUCLEASE T1 ISOZYME


Mass: 11094.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / References: UniProt: P00651, EC: 3.1.27.3
#2: Chemical ChemComp-2GP / GUANOSINE-2'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal grow
*PLUS
Method: other / Details: Heinemann, U., (1980) Eur. J. Biochem., 109, 109.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 6788 / % possible obs: 93 % / Observed criterion σ(I): 1 / Num. measured all: 23819 / Rmerge(I) obs: 0.088

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→6 Å / σ(F): 1 /
RfactorNum. reflection
obs0.191 6788
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms777 0 24 91 892
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d0.037
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONp_planar_d0.060.057
X-RAY DIFFRACTIONp_plane_restr0.020.015
X-RAY DIFFRACTIONp_chiral_restr0.150.15
X-RAY DIFFRACTIONp_mcbond_it10.917
X-RAY DIFFRACTIONp_scbond_it1.51.88
X-RAY DIFFRACTIONp_mcangle_it1.51.494
X-RAY DIFFRACTIONp_scangle_it22.744

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