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- PDB-4rnt: HIS 92 ALA MUTATION IN RIBONUCLEASE T1 INDUCES SEGMENTAL FLEXIBIL... -

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Basic information

Entry
Database: PDB / ID: 4rnt
TitleHIS 92 ALA MUTATION IN RIBONUCLEASE T1 INDUCES SEGMENTAL FLEXIBILITY. AN X-RAY STUDY
ComponentsRIBONUCLEASE T1
KeywordsHYDROLASE(ENDORIBONUCLEASE)
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
Guanyl-specific ribonuclease T1
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSaenger, W. / Koellner, G.
CitationJournal: 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.
History
DepositionFeb 13, 1990Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE T1


Theoretical massNumber of molelcules
Total (without water)11,0281
Polymers11,0281
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.040, 62.310, 43.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES 39 AND 55 ARE CIS PROLINES.

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Components

#1: Protein RIBONUCLEASE T1


Mass: 11027.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / References: UniProt: P00651, EC: 3.1.27.3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1.92 Å3/Da / Density % sol: 35.78 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %protein1drop
220 mMTris-HCl1drop
31 mMEDTA1drop
430 %(w/v)PEG40001drop

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Data collection

Reflection
*PLUS
Num. obs: 982 / Observed criterion σ(F): 1 / Num. measured all: 6189 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.4 Å / % possible obs: 69 %

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2.2→10 Å / σ(I): 0 /
RfactorNum. reflection
obs0.162 3712
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms776 0 0 70 846
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0750.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0720.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9962.5
X-RAY DIFFRACTIONp_mcangle_it2.9193
X-RAY DIFFRACTIONp_scbond_it5.1594.5
X-RAY DIFFRACTIONp_scangle_it6.2656
X-RAY DIFFRACTIONp_plane_restr0.010.015
X-RAY DIFFRACTIONp_chiral_restr0.2440.15
X-RAY DIFFRACTIONp_singtor_nbd0.1550.15
X-RAY DIFFRACTIONp_multtor_nbd0.1490.15
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1670.15
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.83
X-RAY DIFFRACTIONp_staggered_tor21.815
X-RAY DIFFRACTIONp_orthonormal_tor25.520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS

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