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- PDB-3bir: DISECTING HISTIDINE INTERACTIONS IN RIBONUCLEASE T1 BY ASN AND GL... -

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Basic information

Entry
Database: PDB / ID: 3bir
TitleDISECTING HISTIDINE INTERACTIONS IN RIBONUCLEASE T1 BY ASN AND GLN SUBSTITUTIONS
ComponentsRIBONUCLEASE T1
KeywordsENDONUCLEASE / HYDROLASE / RIBONUCLEASE T1 / MUTATION
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: 1.8 Å
AuthorsDoumen, J. / Steyaert, J.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Dissecting histidine interactions of ribonuclease T1 with asparagine and glutamine replacements: analysis of double mutant cycles at one position.
Authors: De Vos, S. / Doumen, J. / Langhorst, U. / Steyaert, J.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: His92Ala Mutation in Ribonuclease T1 Induces Segmental Flexibility. An X-Ray Study
Authors: Koellner, G. / Choe, H.W. / Heinemann, U. / Grunert, H.P. / Zouni, A. / Hahn, U. / Saenger, W.
#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.
#3: Journal: Nature / Year: 1982
Title: Specific Protein-Nucleic Acid Recognition in Ribonuclease T1-2'-Guanylic Acid Complex. An X-Ray Study
Authors: Heinemann, U. / Saenger, W.
History
DepositionJun 27, 1997Processing site: BNL
Revision 1.0Dec 31, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5144
Polymers11,0711
Non-polymers4433
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.160, 46.880, 50.070
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 RIBONUCLEASE T1 / RNASE T1


Mass: 11070.650 Da / Num. of mol.: 1 / Mutation: H92N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / 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.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growpH: 4.2
Details: VAPOR DIFFUSION, NAOAC PH 4.2, 20 MG/ML PROTEIN, 45 % MPD 2.5 MM CACL2, 20 MM GPS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mM1reservoirNaOAc
345 %MPD1reservoir
40.125 %2'-GMP1reservoir
51.25 %1reservoirCaCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 6, 1995 / Details: DUAL SLITS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 4313 / % possible obs: 94 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 14.2 Å2 / Rsym value: 0.107 / Net I/σ(I): 5.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.239 / % possible all: 50
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 8680 / % possible obs: 98.8 % / Num. measured all: 28974 / Rmerge(I) obs: 0.107
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / % possible obs: 95.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
AMoREphasing
X-PLOR3.843refinement
CCP4(ROTAVATA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BIR

1bir


Resolution: 1.8→10 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 475 10 %RANDOM
Rwork0.192 ---
obs0.192 8600 94 %-
Displacement parametersBiso mean: 15.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.58 Å
Luzzati d res low-8 Å
Luzzati sigma a0.31 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms789 29 0 384 1202
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.028
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_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.82
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.421.7
X-RAY DIFFRACTIONx_mcangle_it2.112.3
X-RAY DIFFRACTIONx_scbond_it2.722.3
X-RAY DIFFRACTIONx_scangle_it3.712.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3NUCL.PARAMNUCL.TOPOL
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.82

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