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- PDB-1i0v: Ribonuclease T1 in complex with 2'GMP (form I crystal) -

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Basic information

Entry
Database: PDB / ID: 1i0v
TitleRibonuclease T1 in complex with 2'GMP (form I crystal)
ComponentsGUANYL-SPECIFIC RIBONUCLEASE T1
KeywordsHYDROLASE / ribonuclease / RNase / stability / metal binding / 2'GMP
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 / MOLECULAR REPLACEMENT / Resolution: 1.234 Å
AuthorsDe Swarte, J. / De Vos, S. / Langhorst, U. / Steyaert, J. / Loris, R.
CitationJournal: Eur.J.Biochem. / Year: 2001
Title: The contribution of metal ions to the conformational stability of ribonuclease T1: crystal versus solution.
Authors: Deswarte, J. / De Vos, S. / Langhorst, U. / Steyaert, J. / Loris, R.
History
DepositionJan 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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_atom_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.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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GUANYL-SPECIFIC RIBONUCLEASE T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4983
Polymers11,0951
Non-polymers4032
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.321, 47.609, 50.541
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GUANYL-SPECIFIC RIBONUCLEASE T1 / RNASE T1


Mass: 11094.694 Da / Num. of mol.: 1 / Mutation: Q25K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Production host: Escherichia coli (E. coli) / 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-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.: 124 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: MPD, acetaate, calcium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Zegers, I., (1998) Nat. Struct. Biol., 5, 280.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlRNase T11drop
215 mMexo-cGPS1drop
320 mM1dropNaOAc
42 mM1dropCaCl2
555 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: graphite monochromator
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.23→35 Å / Num. all: 27338 / Num. obs: 27338 / % possible obs: 94.6 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 5.54 % / Biso Wilson estimate: 11.18 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.54
Reflection shellResolution: 1.23→1.27 Å / Redundancy: 3.41 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.81 / Num. unique all: 2147 / % possible all: 75.4
Reflection
*PLUS
Lowest resolution: 38 Å / Num. measured all: 151692
Reflection shell
*PLUS
% possible obs: 75.4 % / Num. unique obs: 2147 / Num. measured obs: 7314 / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.48

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.234→35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1916 2175 random
Rwork0.1783 --
all0.1793 27241 -
obs0.1793 27241 -
Refinement stepCycle: LAST / Resolution: 1.234→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms819 0 49 131 999
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006371
X-RAY DIFFRACTIONc_angle_deg1.61437
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 35 Å / σ(F): 0 / Rfactor obs: 0.1783
Solvent computation
*PLUS
Displacement parameters
*PLUS

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