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- PDB-1lra: CRYSTALLOGRAPHIC STUDY OF GLU 58 ALA RNASE T1(ASTERISK)2'-GUANOSI... -

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Basic information

Entry
Database: PDB / ID: 1lra
TitleCRYSTALLOGRAPHIC STUDY OF GLU 58 ALA RNASE T1(ASTERISK)2'-GUANOSINE MONOPHOSPHATE AT 1.9 ANGSTROMS RESOLUTION
ComponentsRIBONUCLEASE T1
KeywordsHYDROLASE(ENDORIBONUCLEASE)
Function / homology
Function and homology information


hyphal tip / ribonuclease T1 / ribonuclease T1 activity / cell septum / RNA endonuclease activity / lyase 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
GUANOSINE-2'-MONOPHOSPHATE / Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsPletinckx, J. / Steyaert, J. / Choe, H.-W. / Heinemann, U. / Wyns, L.
Citation
Journal: Biochemistry / Year: 1994
Title: Crystallographic study of Glu58Ala RNase T1 x 2'-guanosine monophosphate at 1.9-A resolution.
Authors: Pletinckx, J. / Steyaert, J. / Zegers, I. / Choe, H.W. / Heinemann, U. / Wyns, L.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Three-Dimensional Structure of Ribonuclease T1 Complexed with Guanylyl-2',5'-Guanosine at 1.8 Angstroms Resolution
Authors: Koepke, J. / Maslowska, M. / Heinemann, U. / Saenger, W.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Three-Dimensional Structure of the Ribonuclease T1(Asterisk)2'-Gmp Complex at 1.9-Angstroms Resolution
Authors: Arni, R. / Heinemann, U. / Tokuoka, R. / Saenger, W.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1987
Title: Restrained Least-Squares Refinement of the Crystal Structure of the Ribonuclease T1(Asterisk)2'-Guanylic Acid Complex at 1.9 Angstroms Resolution
Authors: Arni, R. / Heinemann, U. / Maslowska, M. / Tokuoka, R. / 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: J.Biomol.Struct.Dyn. / Year: 1983
Title: Crystallographic Study of Mechanism of Ribonuclease T1-Catalysed Specific RNA Hydrolysis
Authors: Heinemann, U. / Saenger, W.
#6: Journal: Nature / Year: 1982
Title: Specific Protein-Nucleic Acid Recognition in Ribonuclease T1-2'-Guanylic Acid Complex. An X-Ray Study
Authors: Heinemann, U. / Saenger, W.
#7: Journal: Eur.J.Biochem. / Year: 1980
Title: Crystallization of a Complex between Ribonuclease T1 and 2'-Guanylic Acid
Authors: Heinemann, U. / Wernitz, M. / Paehler, A. / Saenger, W. / Menke, G. / Rueterjans, H.
#8: Journal: J.Mol.Biol. / Year: 1991
Title: Ribonuclease T1 with Free Recognition and Catalytic Site: Crystal Structure Analysis at 1.5 Angstroms
Authors: Martinez-Oyanedel, J. / Choe, H.-W. / Heinemann, U. / Saenger, W.
#9: Journal: Biochemistry / Year: 1990
Title: Histidine-40 of Ribonuclease T1Acts as Base Catalyst When the True Catalytic Base, Glutamic Acid 58 is Replaced by Alanine
Authors: Steyaert, J. / Hallenga, K. / Wyns, L. / Stanssens, P.
History
DepositionOct 1, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / 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
Revision 1.4Oct 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 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4233
Polymers11,0371
Non-polymers3862
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.440, 49.640, 26.090
Angle α, β, γ (deg.)90.00, 99.75, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 39 / 2: CIS PROLINE - PRO 55

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Components

#1: Protein RIBONUCLEASE T1


Mass: 11036.658 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-2GP / GUANOSINE-2'-MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 90 / 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

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.41 %
Crystal grow
*PLUS
pH: 4.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 %(w/v)enzyme 1drop
20.125 %2'-GMP1drop
355 %(v/v)MPD1reservoir
420 mMsodium acetate1reservoir
52 mMcalcium acetate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Rmerge(I) obs: 0.069

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.9→10 Å / σ(F): 1 /
RfactorNum. reflection% reflection
obs0.178 5659 77 %
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms773 0 25 90 888
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0590.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0610.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it4.989
X-RAY DIFFRACTIONp_mcangle_it5.694
X-RAY DIFFRACTIONp_scbond_it6.374
X-RAY DIFFRACTIONp_scangle_it7.977
X-RAY DIFFRACTIONp_plane_restr0.010.015
X-RAY DIFFRACTIONp_chiral_restr0.2130.15
X-RAY DIFFRACTIONp_singtor_nbd0.1370.15
X-RAY DIFFRACTIONp_multtor_nbd0.130.15
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1520.15
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.73
X-RAY DIFFRACTIONp_staggered_tor16.112
X-RAY DIFFRACTIONp_orthonormal_tor21.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 10 Å / Num. reflection obs: 5659 / σ(F): 1 / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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