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- PDB-4bir: RIBONUCLEASE T1: FREE HIS92GLN MUTANT -

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Basic information

Entry
Database: PDB / ID: 4bir
TitleRIBONUCLEASE T1: FREE HIS92GLN MUTANT
ComponentsGUANYL-SPECIFIC RIBONUCLEASE T1
KeywordsENDORIBONUCLEASE / HYDROLASE / RIBONUCLEASE / HIS TO GLN MUTANT
Function / homology
Function and homology information


hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / endonuclease activity / lyase activity / RNA binding
Similarity search - Function
: / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDoumen, J. / Steyaert, J.
Citation
Journal: Biochemistry / Year: 1992
Title: Role of histidine-40 in ribonuclease T1 catalysis: three-dimensionalstructures of the partially active His40Lys mutant.
Authors: Zegers, I. / Verhelst, P. / Choe, H.W. / Steyaert, J. / Heinemann, U. / Saenger, W. / Wyns, L.
#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
DepositionJan 13, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Refinement description / Category: diffrn_detector / pdbx_database_status / software
Item: _diffrn_detector.detector / _pdbx_database_status.process_site / _software.name
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_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.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.value / _struct_conn.pdbx_dist_value / _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_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 1.5Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GUANYL-SPECIFIC RIBONUCLEASE T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1252
Polymers11,0851
Non-polymers401
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.820, 46.530, 41.200
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 GUANYL-SPECIFIC RIBONUCLEASE T1 / RNASE T1


Mass: 11084.676 Da / Num. of mol.: 1 / Mutation: H92Q
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.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growpH: 4.2 / Details: pH 4.2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceType: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 5, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 10404 / % possible obs: 93.9 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Rsym value: 0.079 / Net I/σ(I): 6.5
Reflection shellResolution: 1.68→1.73 Å / Redundancy: 2.18 % / Mean I/σ(I) obs: 3 / Rsym value: 0.257 / % possible all: 51.3

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Processing

Software
NameVersionClassification
Agrovatadata collection
ROTAVATAdata reduction
FROFFTmodel building
PROFFTrefinement
CCP4(ROTAVATA)data scaling
FROFFTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RGA

1rga


Resolution: 1.7→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rwork0.187 ---
all-4313 --
obs-4313 94.5 %-
Rfree---RANDOM
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms785 0 0 147 932
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0760.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0880.05
X-RAY DIFFRACTIONp_hb_or_metal_coord00.05
X-RAY DIFFRACTIONp_mcbond_it2.1772
X-RAY DIFFRACTIONp_mcangle_it2.8473
X-RAY DIFFRACTIONp_scbond_it3.8093
X-RAY DIFFRACTIONp_scangle_it4.7244
X-RAY DIFFRACTIONp_plane_restr0.0130.015
X-RAY DIFFRACTIONp_chiral_restr0.1750.15
X-RAY DIFFRACTIONp_singtor_nbd0.1380.15
X-RAY DIFFRACTIONp_multtor_nbd0.1270.15
X-RAY DIFFRACTIONp_xhyhbond_nbd00.15
X-RAY DIFFRACTIONp_xyhbond_nbd0.1390.15
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor1312
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.720
X-RAY DIFFRACTIONp_special_tor015

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