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- PDB-3rsd: STRUCTURE OF THE D121N VARIANT OF RIBONUCLEASE A -

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Basic information

Entry
Database: PDB / ID: 3rsd
TitleSTRUCTURE OF THE D121N VARIANT OF RIBONUCLEASE A
ComponentsRIBONUCLEASE A
KeywordsHYDROLASE / ENDONUCLEASE / RIBONUCLEASE A / SITE-DIRECTED MUTAGENESIS
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchultz, L.W. / Quirk, D.J. / Raines, R.T.
CitationJournal: Biochemistry / Year: 1998
Title: His...Asp catalytic dyad of ribonuclease A: structure and function of the wild-type, D121N, and D121A enzymes.
Authors: Schultz, L.W. / Quirk, D.J. / Raines, R.T.
History
DepositionFeb 5, 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 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: RIBONUCLEASE A


Theoretical massNumber of molelcules
Total (without water)13,7071
Polymers13,7071
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.520, 38.400, 53.310
Angle α, β, γ (deg.)90.00, 105.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RIBONUCLEASE A


Mass: 13707.342 Da / Num. of mol.: 1 / Mutation: D121N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line: BL21 / Organ: PANCREAS / Plasmid: PBXR / Species (production host): Escherichia coli / Cellular location (production host): INCLUSION BODIES / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P61823, EC: 3.1.27.5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.19 Å3/Da / Density % sol: 60 %
Crystal growMethod: batch method / pH: 5.2
Details: LYOPHILIZED D121N RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ ML. CRYSTALLIZATION WAS PERFORMED IN SMALL SILICONIZED TUBES USING THE BATCH METHOD. A SOLUTION (25UL) ...Details: LYOPHILIZED D121N RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ ML. CRYSTALLIZATION WAS PERFORMED IN SMALL SILICONIZED TUBES USING THE BATCH METHOD. A SOLUTION (25UL) OF THE ENZYME WAS MIXED WITH AN EQUAL VOLUME OF 95% (V/V) 2-METHYL-2,4-PENTANEDIOL IN 0.10 M MES BUFFER, PH 5.2. CRYSTALS APPEARED WITHIN SEVERAL MONTHS., batch method
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlenzyme11
247.5 %(v/v)MPD11
30.05 MMES-NaOH11

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 28, 1995 / Details: LONG MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 15756 / % possible obs: 88 % / Observed criterion σ(I): 0.33 / Redundancy: 1.8 % / Rsym value: 0.019 / Net I/σ(I): 31
Reflection shellResolution: 1.6→1.7 Å / Rsym value: 0.057 / % possible all: 75
Reflection
*PLUS
% possible obs: 89 % / Num. measured all: 28480 / Rmerge(I) obs: 0.019
Reflection shell
*PLUS
Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
XDSdata scaling
XCALIBREdata reduction
AMoREphasing
TNT5Erefinement
XDSdata reduction
XCALIBREdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RPH

1rph


Resolution: 1.6→30 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.177 15756 -
obs-15756 88 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 257 Å2 / ksol: 0.75 e/Å3
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 0 100 1056
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0119805
X-RAY DIFFRACTIONt_angle_deg2.1513238
X-RAY DIFFRACTIONt_dihedral_angle_d17.15970
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0052825
X-RAY DIFFRACTIONt_gen_planes0.00914050
X-RAY DIFFRACTIONt_it1
X-RAY DIFFRACTIONt_nbd0.026950
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.10
X-RAY DIFFRACTIONt_planar_d0.00525
X-RAY DIFFRACTIONt_plane_restr0.00950

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