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- PDB-1bir: RIBONUCLEASE T1, PHE 100 TO ALA MUTANT COMPLEXED WITH 2' GMP -

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Basic information

Entry
Database: PDB / ID: 1bir
TitleRIBONUCLEASE T1, PHE 100 TO ALA MUTANT COMPLEXED WITH 2' GMP
ComponentsRIBONUCLEASE T1
KeywordsENDORIBONUCLEASE / HYDROLASE / NUCLEASE
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 / Resolution: 1.8 Å
AuthorsDoumen, J. / Gonciarz, M. / Zegers, I. / Loris, R. / Wyns, L. / Steyaert, J.
Citation
Journal: Protein Sci. / Year: 1996
Title: A catalytic function for the structurally conserved residue Phe 100 of ribonuclease T1.
Authors: Doumen, J. / Gonciarz, M. / Zegers, I. / Loris, R. / Wyns, L. / Steyaert, J.
#1: Journal: Biochemistry / Year: 1992
Title: Role of Histidine-40 in Ribonuclease T1 Catalysis: Three-Dimensional Structures of the Partially Active His40Lys Mutant
Authors: Zegers, I. / Verhelst, P. / Choe, H.W. / Steyaert, J. / Heinemann, U. / Saenger, W. / Wyns, L.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Three-Dimensional Structure of the Ribonuclease T1 2'-Gmp Complex at 1.9-A Resolution
Authors: Arni, R. / Heinemann, U. / Tokuoka, R. / Saenger, W.
History
DepositionJan 4, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.4Nov 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.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 1.5Nov 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

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE T1
B: RIBONUCLEASE T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8446
Polymers22,0372
Non-polymers8074
Water2,504139
1
A: RIBONUCLEASE T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4223
Polymers11,0191
Non-polymers4032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIBONUCLEASE T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4223
Polymers11,0191
Non-polymers4032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.200, 48.190, 40.160
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9963, 0.0852, -0.0065), (-0.0851, -0.9963, -0.0077), (-0.0072, -0.0071, 0.9999)
Vector: 24.4746, 2.1411, -19.7745)

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Components

#1: Protein RIBONUCLEASE T1 / RNASE T1


Mass: 11018.598 Da / Num. of mol.: 2 / Mutation: F100A
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH 2'-GMP / Source: (gene. exp.) Aspergillus oryzae (mold)
Description: STEYAERT ET AL. (1990) BIOCHEMISTRY 29, 9064-9072
Gene: SYNTHETIC GENE / Plasmid: PMC5-RT1 / Gene (production host): SYNTHETIC GENE / 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.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal grow
*PLUS
pH: 4.2 / Method: vapor diffusion, sitting drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlrecombinant Phe 100 Ala RNase T11drop
21.25 %(w/v)2'-GMP1drop
325 mMsodium acetate1drop
42.5 mMcalcium acetate1drop
552.5 %MPD1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.056
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 17890 / % possible obs: 99.7 % / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Highest resolution: 1.82 Å / Lowest resolution: 1.9 Å / % possible obs: 100 % / Rmerge(I) obs: 0.056

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 1.8→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.24 -10 %
Rwork0.186 --
obs0.186 17686 -
Displacement parametersBiso mean: 14.84 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 48 0 115 1713
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.835
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
X-RAY DIFFRACTIONx_improper_angle_deg1.755

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