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- PDB-4hoh: RIBONUCLEASE T1 (THR93ALA MUTANT) COMPLEXED WITH 2'GMP -

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Basic information

Entry
Database: PDB / ID: 4hoh
TitleRIBONUCLEASE T1 (THR93ALA MUTANT) COMPLEXED WITH 2'GMP
ComponentsPROTEIN (RIBONUCLEASE T1)
KeywordsHYDROLASE / ENDORIBONUCLEASE / RIBONUCLEASE / ENDONUCLEASE
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: 2.05 Å
AuthorsLanghorst, U. / Loris, R. / Denisov, V.P. / Doumen, J. / Roose, P. / Maes, D. / Halle, B. / Steyaert, J.
CitationJournal: Protein Sci. / Year: 1999
Title: Dissection of the structural and functional role of a conserved hydration site in RNase T1.
Authors: Langhorst, U. / Loris, R. / Denisov, V.P. / Doumen, J. / Roose, P. / Maes, D. / Halle, B. / Steyaert, J.
History
DepositionSep 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 23, 1998Provider: 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.ptnr1_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_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 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 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
A: PROTEIN (RIBONUCLEASE T1)
B: PROTEIN (RIBONUCLEASE T1)
C: PROTEIN (RIBONUCLEASE T1)
D: PROTEIN (RIBONUCLEASE T1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,15511
Polymers44,2594
Non-polymers1,8967
Water3,945219
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A: PROTEIN (RIBONUCLEASE T1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4282
Polymers11,0651
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (RIBONUCLEASE T1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4282
Polymers11,0651
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (RIBONUCLEASE T1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8314
Polymers11,0651
Non-polymers7673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PROTEIN (RIBONUCLEASE T1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4683
Polymers11,0651
Non-polymers4032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.320, 60.310, 101.030
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(-0.110694, -0.811065, -0.574387), (0.869585, -0.358873, 0.339164), (-0.481216, -0.461935, 0.745015)53.41301, 64.77747, -10.28357
2given(0.570249, 0.809786, 0.138068), (-0.425493, 0.434937, -0.79359), (-0.702689, 0.393797, 0.592581)55.2653, -57.90049, 57.12147
3given(-0.035199, 0.853298, 0.520234), (-0.887029, 0.213122, -0.409582), (-0.460369, -0.47588, 0.749399)83.33276, 1.90023, 35.92253

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Components

#1: Protein
PROTEIN (RIBONUCLEASE T1) / RNASE T1


Mass: 11064.668 Da / Num. of mol.: 4 / Mutation: T93A
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH GUANOSINE-2'-MONOPHOSPHATE / Source: (gene. exp.) Aspergillus oryzae (mold) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 / References: UniProt: P00651, EC: 3.1.27.3
#2: Chemical
ChemComp-2GP / GUANOSINE-2'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.04 Å3/Da / Density % sol: 39.73 %
Crystal growpH: 4.2 / Details: pH 4.20
Crystal grow
*PLUS
pH: 4.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
225 mM11NaAc
32.8 mM2'GMP11
46.25 mM11CaCl2
542.5 %MPD11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: DUAL SLITS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→15 Å / Num. obs: 21739 / % possible obs: 92.8 % / Redundancy: 2.95 % / Rsym value: 0.065 / Net I/σ(I): 11.9
Reflection shellResolution: 2.05→2.14 Å / Redundancy: 2.29 % / Mean I/σ(I) obs: 5.25 / Rsym value: 0.217 / % possible all: 80.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RGA

1rga


Resolution: 2.05→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1457 6.7 %RANDOM
Rwork0.19 ---
obs0.19 21739 92.8 %-
Refinement stepCycle: LAST / Resolution: 2.05→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 122 219 3441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.82
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.07
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
LS refinement shellResolution: 2.05→2.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.269 141 6.2 %
Rwork0.253 2280 -
obs--80.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO

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