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- PDB-1lov: X-ray structure of the E58A mutant of Ribonuclease T1 complexed w... -

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Basic information

Entry
Database: PDB / ID: 1lov
TitleX-ray structure of the E58A mutant of Ribonuclease T1 complexed with 3'-guanosine monophosphate
ComponentsGuanyl-specific ribonuclease T1
KeywordsHYDROLASE / RNase / catalytic dyad / nucleophile activation / ab initio calculations
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-3'-MONOPHOSPHATE / Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMignon, P. / Steyaert, J. / Loris, R. / Geerlings, P. / Loverix, S.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study
Authors: Mignon, P. / Steyaert, J. / Loris, R. / Geerlings, P. / Loverix, S.
History
DepositionMay 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999 The isozyme of RNase T1 used here contains a lysine at position 25.

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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)11,4403
Polymers11,0371
Non-polymers4032
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.631, 48.126, 53.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Guanyl-specific ribonuclease T1 / RNAse T1


Mass: 11036.658 Da / Num. of mol.: 1 / Mutation: E58A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Plasmid: pMC / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 / 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-3GP / GUANOSINE-3'-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.: 75 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: MPD,CaCl2,sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.5 mMprotein1drop
23 mMsubstrate1drop
32 mM1reservoirCaCl2
450 mMsodium acetate1reservoirpH4.2
542-52 %MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 2000
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 15601 / Num. obs: 15601 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.317 / % possible all: 97.2
Reflection
*PLUS
Num. obs: 15595 / % possible obs: 99.45 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RGA

1rga


Resolution: 1.55→30 Å / Cross valid method: THROUGHOUT / σ(F): 0.001 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.199 3221 Random
Rwork0.187 --
all0.19 15595 -
obs0.19 15595 -
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms777 0 25 75 877
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004894
X-RAY DIFFRACTIONc_angle_d1.38188
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4

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