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- PDB-1b2m: THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ... -

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Basic information

Entry
Database: PDB / ID: 1b2m
TitleTHREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.
Components
  • 5'-R(*GP*(U34))-3'
  • RIBONUCLEASE T1
KeywordsHYDROLASE/RNA / HYDROLASE / ENDORIBONUCLEASE / HYDROLASE-RNA complex
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
RNA / Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsArni, R.K. / Watanabe, L. / Ward, R.J. / Kreitman, R.J. / Kumar, K. / Walz Jr., F.G.
Citation
Journal: Biochemistry / Year: 1999
Title: Three-dimensional structure of ribonuclease T1 complexed with an isosteric phosphonate substrate analogue of GpU: alternate substrate binding modes and catalysis.
Authors: Arni, R.K. / Watanabe, L. / Ward, R.J. / Kreitman, R.J. / Kumar, K. / Walz Jr., F.G.
#1: Journal: Biochemistry / Year: 1992
Title: Three-Dimensional Structure of Gln 25-Ribonuclease T1 at 1.84 Angstroms Resolution: Structural Variations at the Base Recognition and Catalytic Sites
Authors: Arni, R.K. / Pal, G.P. / Ravichandran, K.G. / Tulinsky, A. / Metcalf Jr., P.F.G.W.
#2: 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.
#3: Journal: J.Biol.Chem. / Year: 1988
Title: Three Dimensional Structures of the Ribonuclease T1 2'-Gmp Complex at 1.9 Angstroms Resolution
Authors: Arni, R. / Heinemann, U. / Tokuoka, R. / Saenger, W.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1987
Title: Restrained Least-Squares Refinement of the Crystal Structure of the Ribonuclease T1 2'-Guanylic Acid Complex at 1.9 Angstroms Resolution
Authors: Arni, R. / Heinemann, V. / Maslowska, M. / Tokuoka, R. / Saenger, W.
#5: Journal: Fresenius Z.Anal.Chem. / Year: 1987
Title: Structure and Function of the Enzyme Ribonuclease T1
Authors: Arni, R. / Heinemann, U. / Saenger, W.
#6: Journal: J.Mol.Biol. / Year: 1980
Title: Crystallization of Ribonuclease T1
Authors: Martin, P.O. / Tulinsky, A. / Walz, F.G.
History
DepositionNov 27, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-R(*GP*(U34))-3'
D: 5'-R(*GP*(U34))-3'
E: 5'-R(*GP*(U34))-3'
A: RIBONUCLEASE T1
B: RIBONUCLEASE T1


Theoretical massNumber of molelcules
Total (without water)24,0495
Polymers24,0495
Non-polymers00
Water1,65792
1
C: 5'-R(*GP*(U34))-3'
A: RIBONUCLEASE T1


Theoretical massNumber of molelcules
Total (without water)11,7142
Polymers11,7142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 5'-R(*GP*(U34))-3'
E: 5'-R(*GP*(U34))-3'
B: RIBONUCLEASE T1


Theoretical massNumber of molelcules
Total (without water)12,3353
Polymers12,3353
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.910, 90.290, 33.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.0701, 0.9676, -0.2427), (-0.5247, 0.1711, 0.8339), (0.8484, 0.1858, 0.4957)51.299, 4.649, -14.759
2given(0.5413, 0.6404, 0.5469), (0.0409, 0.6272, -0.7778), (-0.8398, 0.4433, 0.3133)-16.614, 43.666, 67.113

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Components

#1: RNA chain 5'-R(*GP*(U34))-3'


Mass: 620.441 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: Protein RIBONUCLEASE T1


Mass: 11093.644 Da / Num. of mol.: 2 / Mutation: GLN 25 VARIANT / Source method: isolated from a natural source / Details: RNASE T1 COMPLEXED WITH 5'-R(*GP*(CH2)U)-3 / Source: (natural) Aspergillus oryzae (mold) / References: UniProt: P00651, EC: 3.1.27.3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growpH: 4.1 / Details: pH 4.10
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM ACETATE11
2TRIS11
3MGCL211
4PEG 400011
5PEG 400012
Crystal grow
*PLUS
pH: 4.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMsodium acetate1drop
210 mg/mlprotein1drop
30.1 MTris-HCl1reservoir
40.2 M1reservoirMgCl2
530 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 11298 / % possible obs: 75 % / Observed criterion σ(I): 2 / Rsym value: 0.64
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % possible obs: 75 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RNT

1rnt


Resolution: 2→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.254 -10 %RANDOM
Rwork0.187 ---
obs0.187 9879 75 %-
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 120 0 92 1774
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.74
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.42
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. reflection obs: 26734
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.42

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