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- PDB-1i0x: RIBONUCLEASE T1 IN COMPLEX WITH 2'GMP (FORM II CRYSTAL) -

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Basic information

Entry
Database: PDB / ID: 1i0x
TitleRIBONUCLEASE T1 IN COMPLEX WITH 2'GMP (FORM II CRYSTAL)
ComponentsGUANYL-SPECIFIC RIBONUCLEASE T1
KeywordsHYDROLASE / Ribonuclease / RNase / metal binding / stability / 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: 1.65 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_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 1.4Nov 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
B: GUANYL-SPECIFIC RIBONUCLEASE T1
C: GUANYL-SPECIFIC RIBONUCLEASE T1
D: GUANYL-SPECIFIC RIBONUCLEASE T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,39514
Polymers44,3794
Non-polymers2,01610
Water9,530529
1
A: GUANYL-SPECIFIC RIBONUCLEASE T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4582
Polymers11,0951
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GUANYL-SPECIFIC RIBONUCLEASE T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5384
Polymers11,0951
Non-polymers4433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GUANYL-SPECIFIC RIBONUCLEASE T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8614
Polymers11,0951
Non-polymers7673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GUANYL-SPECIFIC RIBONUCLEASE T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5384
Polymers11,0951
Non-polymers4433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: GUANYL-SPECIFIC RIBONUCLEASE T1
hetero molecules

C: GUANYL-SPECIFIC RIBONUCLEASE T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3998
Polymers22,1892
Non-polymers1,2106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x+1/2,-y+3/2,-z+11
Buried area2980 Å2
ΔGint-43 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.271, 59.696, 100.136
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.: 4 / 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-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.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 1.96 Å3/Da / Density % sol: 37.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: MPD, acetate, calcium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 11, 1998 / 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: 1.65→15 Å / Num. all: 40949 / Num. obs: 40949 / % possible obs: 95.7 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 5.55 % / Biso Wilson estimate: 13.67 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.81
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 5.36 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.72 / Num. unique all: 3920 / % possible all: 92.4
Reflection
*PLUS
Num. obs: 41132 / Num. measured all: 228296 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 92.4 % / Num. unique obs: 3920 / Num. measured obs: 20995

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.216 2873 random
Rwork0.1903 --
all0.1921 228296 -
obs0.1921 40949 -
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 125 529 3750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.1903 / Rfactor Rfree: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.571

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