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- PDB-4rsd: STRUCTURE OF THE D121A VARIANT OF RIBONUCLEASE A -

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Basic information

Entry
Database: PDB / ID: 4rsd
TitleSTRUCTURE OF THE D121A VARIANT OF RIBONUCLEASE A
ComponentsRIBONUCLEASE APancreatic ribonuclease family
KeywordsHYDROLASE / ENDONUCLEASE / RIBONUCLEASE A / SITE-DIRECTED MUTAGENESIS
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / 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
ACETATE ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (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 / Derived calculations / Category: database_2 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7944
Polymers13,6641
Non-polymers1303
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.700, 64.700, 65.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RIBONUCLEASE A / Pancreatic ribonuclease family


Mass: 13664.316 Da / Num. of mol.: 1 / Mutation: D121A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (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: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.87 Å3/Da / Density % sol: 60 %
Crystal growpH: 5.3
Details: DROPS CONSISTING OF 1.5UL OF A 60MG/ML PROTEIN SOLUTION, 1.5UL OF H2O AND 3UL OF RESERVOIR SOLUTION WERE SUSPENDED OVER A 0.5ML RESERVOIR CONTAINING A SOLUTION OF 2.5M NAOAC, PH 5.3 IN ...Details: DROPS CONSISTING OF 1.5UL OF A 60MG/ML PROTEIN SOLUTION, 1.5UL OF H2O AND 3UL OF RESERVOIR SOLUTION WERE SUSPENDED OVER A 0.5ML RESERVOIR CONTAINING A SOLUTION OF 2.5M NAOAC, PH 5.3 IN SATURATING NACL. TEMP. 20C.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
32.5 Msodium acetate1reservoir
1enzyme solution1drop0.0015ml
2water1drop0.0015ml
41reservoirsaturatingNaCl

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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: Feb 7, 1996 / 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: 27087 / % possible obs: 91 % / Observed criterion σ(I): 0.33 / Redundancy: 2.1 % / Rsym value: 0.029 / Net I/σ(I): 20
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.14 / % possible all: 85
Reflection
*PLUS
Num. measured all: 56287 / Rmerge(I) obs: 0.029
Reflection shell
*PLUS
Rmerge(I) obs: 0.2

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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 / Details: ASP 83 IS MODELED WITH TWO DIFFERENT POSITIONS.
RfactorNum. reflection% reflection
all0.18 19996 -
obs-19996 91 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 164 Å2 / ksol: 0.79 e/Å3
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms953 0 6 102 1061
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0139818
X-RAY DIFFRACTIONt_angle_deg2.7813267
X-RAY DIFFRACTIONt_dihedral_angle_d16.85970
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0072825
X-RAY DIFFRACTIONt_gen_planes0.01114350
X-RAY DIFFRACTIONt_it1
X-RAY DIFFRACTIONt_nbd0.0461650
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.80
X-RAY DIFFRACTIONt_planar_d0.00725
X-RAY DIFFRACTIONt_plane_restr0.01150

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