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- PDB-1det: RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP -

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Basic information

Entry
Database: PDB / ID: 1det
TitleRIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP
ComponentsRIBONUCLEASE T1
KeywordsHYDROLASE (ENDORIBONUCLEASE) / HYDROLASE / ENDORIBONUCLEASE / NUCLEASE / ENDONUCLEASE
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 / SYNCHROTRON / Resolution: 1.8 Å
AuthorsIshikawa, K. / Suzuki, E. / Tanokura, M. / Takahashi, K.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystal structure of ribonuclease T1 carboxymethylated at Glu58 in complex with 2'-GMP.
Authors: Ishikawa, K. / Suzuki, E. / Tanokura, M. / Takahashi, K.
#1: Journal: Eur.J.Biochem. / Year: 1993
Title: Three-Dimensional Structure of the Ternary Complex between Ribonuclease T1, Guanosine 3',5'-Bisphosphate and Inorganic Phosphate at 0.19 Nm Resolution
Authors: Lenz, A. / Choe, H.W. / Granzin, J. / Heinemann, U. / Saenger, W.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: X-Ray Analysis of Cubic Crystals of the Complex Formed between Ribonuclease T1 and Guanosine-3',5'-Bisphosphate
Authors: Lenz, A. / Heinemann, U. / Maslowska, M. / Saenger, W.
#3: 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.
History
DepositionFeb 20, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.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)11,5614
Polymers11,1521
Non-polymers4093
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.690, 88.690, 88.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein RIBONUCLEASE T1 / RNASE T1


Mass: 11151.681 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE G-CARBOXYL GROUP OF GLU 58 IS CARBOXYMETHYLATED
Source: (natural) Aspergillus oryzae (mold) / References: UniProt: P00651, EC: 3.1.27.3
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / 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.: 79 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal
*PLUS
Density % sol: 52.9 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 3.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.5 %2'-GMP1drop
330 mMsodium citrate1drop
417 %(v/v)2-methylpentane-2,4-diol1drop
551 %(v/v)2-methylpentane-2,4-diol1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 16, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 10459 / % possible obs: 95.9 % / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.89 Å / % possible obs: 89.7 %

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Processing

Software
NameClassification
WEISdata collection
PROLSQrefinement
WEISdata reduction
RefinementResolution: 1.8→8 Å / σ(F): 1 /
Num. reflection% reflection
obs10354 96 %
Displacement parametersBiso mean: 32.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms783 24 4 81 892
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0450.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4241
X-RAY DIFFRACTIONp_mcangle_it2.4241.5
X-RAY DIFFRACTIONp_scbond_it2.5471.5
X-RAY DIFFRACTIONp_scangle_it3.9952
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1910.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.1960.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2340.3
X-RAY DIFFRACTIONp_planar_tor2.93
X-RAY DIFFRACTIONp_staggered_tor17.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2620
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.194 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

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