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- PDB-3rnt: CRYSTAL STRUCTURE OF GUANOSINE-FREE RIBONUCLEASE T1, COMPLEXED WI... -

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Basic information

Entry
Database: PDB / ID: 3rnt
TitleCRYSTAL STRUCTURE OF GUANOSINE-FREE RIBONUCLEASE T1, COMPLEXED WITH VANADATE(V), SUGGESTS CONFORMATIONAL CHANGE UPON SUBSTRATE BINDING
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
VANADATE ION / Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsKostrewa, D. / Choe, H.-W. / Heinemann, U. / Saenger, W.
Citation
Journal: Biochemistry / Year: 1989
Title: Crystal structure of guanosine-free ribonuclease T1, complexed with vanadate (V), suggests conformational change upon substrate binding.
Authors: Kostrewa, D. / Choe, H.W. / Heinemann, U. / Saenger, W.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Three-Dimensional Structure of Ribonuclease T1 Complexed with Guanylyl-2(Prime),5(Prime)-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(Prime)-Gmp Complex at 1.9-Angstroms Resolution
Authors: Arni, R. / Heinemann, U. / Tokuoka, R. / Saenger, W.
#3: Journal: Fresenius Z.Anal.Chem. / Year: 1987
Title: Struktur Und Funktion Des Enzyms Ribonuclease T1 (German)
Authors: Arni, R. / Heinemann, U. / Saenger, W.
#4: 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.
#5: Journal: Pure Appl.Chem. / Year: 1985
Title: Mechanism of Guanosine Recognition and RNA Hydrolysis by Ribonuclease T1
Authors: Heinemann, U. / Saenger, W.
#6: 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.
#7: Journal: Jerusalem Symp.Quantum Chem.Biochem. / Year: 1983
Title: Ribonuclease T1. Mechanism of Specific Guanine Recognition and RNA Hydrolysis
Authors: Heinemann, U. / Saenger, W.
#8: Journal: J.Biomol.Struct.Dyn. / Year: 1983
Title: Crystallographic Study of Mechanism of Ribonuclease T1-Catalysed Specific RNA Hydrolysis
Authors: Heinemann, U. / Saenger, W.
#9: 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.
#10: 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
DepositionMay 31, 1989Processing site: BNL
Revision 1.0Oct 15, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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
Revision 1.4Oct 9, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)11,2503
Polymers11,0951
Non-polymers1552
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.820, 46.530, 41.200
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


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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal grow
*PLUS
pH: 5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11-2 %(w/v)RNaseT11drop
210 mMsodium acetate1reservoir
32 mM1reservoirCaCl2
41 mM1reservoirNaN3
555 %(v/v)MPD1drop

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 7134 / % possible obs: 77 % / Observed criterion σ(F): 1 / Num. measured all: 11536
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 2 Å / % possible obs: 59 %

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.8→10 Å / σ(I): 0 /
RfactorNum. reflection
obs0.137 7070
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms786 0 6 162 954
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0250.02
X-RAY DIFFRACTIONp_angle_d0.0610.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0670.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.1232
X-RAY DIFFRACTIONp_mcangle_it2.6983
X-RAY DIFFRACTIONp_scbond_it4.7064.5
X-RAY DIFFRACTIONp_scangle_it6.0346
X-RAY DIFFRACTIONp_plane_restr0.0120.015
X-RAY DIFFRACTIONp_chiral_restr0.2490.15
X-RAY DIFFRACTIONp_singtor_nbd0.1310.15
X-RAY DIFFRACTIONp_multtor_nbd0.1380.15
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1580.15
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.93
X-RAY DIFFRACTIONp_staggered_tor2015
X-RAY DIFFRACTIONp_orthonormal_tor22.820
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
σ(I): 1 / Rfactor obs: 0.137
Solvent computation
*PLUS
Displacement parameters
*PLUS

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