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- PDB-1ch0: RNASE T1 VARIANT WITH ALTERED GUANINE BINDING SEGMENT -

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Basic information

Entry
Database: PDB / ID: 1ch0
TitleRNASE T1 VARIANT WITH ALTERED GUANINE BINDING SEGMENT
ComponentsPROTEIN (RIBONUCLEASE T1)
KeywordsHYDROLASE / RIBONUCLEASE
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: 2.3 Å
AuthorsHoeschler, K. / Hoier, H. / Orth, P. / Hubner, B. / Saenger, W. / Hahn, U.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structural analysis of an RNase T1 variant with an altered guanine binding segment.
Authors: Hoschler, K. / Hoier, H. / Hubner, B. / Saenger, W. / Orth, P. / Hahn, U.
History
DepositionMar 30, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (RIBONUCLEASE T1)
B: PROTEIN (RIBONUCLEASE T1)
C: PROTEIN (RIBONUCLEASE T1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,35410
Polymers33,4313
Non-polymers9227
Water2,594144
1
A: PROTEIN (RIBONUCLEASE T1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5473
Polymers11,1441
Non-polymers4032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (RIBONUCLEASE T1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1842
Polymers11,1441
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (RIBONUCLEASE T1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6235
Polymers11,1441
Non-polymers4794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.820, 48.850, 158.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.45979, 0.88686, -0.04563), (-0.88387, 0.462, 0.07306), (0.08587, 0.00673, 0.99628)-17.87701, 18.95935, -27.22359
2given(-0.6148, 0.77397, 0.15162), (-0.78022, -0.62494, 0.02643), (0.11521, -0.10205, 0.98808)-13.5807, 47.96136, -51.07716

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Components

#1: Protein PROTEIN (RIBONUCLEASE T1)


Mass: 11143.771 Da / Num. of mol.: 3 / Mutation: Q25K, K41E, Y42F, N43R, Y45W, E46Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Description: SYNTHETIC GENE / Production host: Escherichia coli (E. coli)
Strain (production host): PA2T1 (QUAAS EUR. J. BIOCHEM. V.173 PP.617-622)
References: UniProt: P00651, EC: 3.1.27.3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-2GP / GUANOSINE-2'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PROTEIN USED IN THIS STUDY IS THE ISOZYME OF RIBONUCLEASE T1 WHERE A LYSINE RESIDUE REPLACES ...THE PROTEIN USED IN THIS STUDY IS THE ISOZYME OF RIBONUCLEASE T1 WHERE A LYSINE RESIDUE REPLACES GLUTAMINE 25 OF THE SEQUENCED RIBONUCLEASE T1 (K.TAKAHASHI, J.BIOCHEM.,V. 98, P. 815, 1985).

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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: 2.31 Å3/Da / Density % sol: 36 %
Crystal growpH: 7.7
Details: HANGING DROP CONTAINING 2.5 MG/ML RNASE T1, 2.5 MG/ML 2GMP, 15% PEG MONOMETHYLETHER 5000, 50 MM TRIS/HCL (PH7.7), 50 MM MGCL2, 50 MM CACL2 AGAINST 30 % PEG MONOMETHYLETHER 5000, 100 MM ...Details: HANGING DROP CONTAINING 2.5 MG/ML RNASE T1, 2.5 MG/ML 2GMP, 15% PEG MONOMETHYLETHER 5000, 50 MM TRIS/HCL (PH7.7), 50 MM MGCL2, 50 MM CACL2 AGAINST 30 % PEG MONOMETHYLETHER 5000, 100 MM TRIS/HCL (PH7.7), 100 MM MGCL2, 100 MM CACL2
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1dropin water
210 mg/ml2'-GMP1dropin water
330 %(w/v)mPEG50001reservoir
4100 mMTris-HCl1reservoirpH7.7
5100 mM1reservoirMgCl2
6100 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→35.6 Å / Num. obs: 14434 / % possible obs: 97.7 % / Redundancy: 3.14 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.115 / Net I/σ(I): 9.04
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.396 / % possible all: 98.1
Reflection
*PLUS
Rmerge(I) obs: 0.115
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.396

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RNT

1rnt


Resolution: 2.3→35.6 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: PARAMETER AND TOPOLOGY FILES FOR 2'GMP WERE OBTAINED FROM HTTP:// ALPHA2.BMC.UU.SE/HICUP/
RfactorNum. reflection% reflectionSelection details
Rfree0.241 812 5.6 %RANDOM
Rwork0.198 ---
obs-14131 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.9 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso mean: 34.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 53 144 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.2
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_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.6821.5
X-RAY DIFFRACTIONx_mcangle_it2.6692
X-RAY DIFFRACTIONx_scbond_it2.5372
X-RAY DIFFRACTIONx_scangle_it3.6782.5
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.287 96 5.3 %
Rwork0.254 1636 -
obs--95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMPROTEIN.LINK
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION42GP_XPLOR_PAR.TXT2GP_XPLOR_TOP.TXT
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 35.6 Å / σ(F): 0 / % reflection Rfree: 5.6 % / Rfactor obs: 0.241 / Rfactor Rfree: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Rfactor Rfree: 0.287 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.254

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