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- PDB-3rsp: STRUCTURE OF THE P93G VARIANT OF RIBONUCLEASE A -

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Basic information

Entry
Database: PDB / ID: 3rsp
TitleSTRUCTURE OF THE P93G VARIANT OF RIBONUCLEASE A
ComponentsRIBONUCLEASE A
KeywordsENDONUCLEASE / HYDROLASE / 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: 1.7 Å
AuthorsSchultz, L.W. / Hargraves, S.R. / Klink, T.A. / Raines, R.T.
CitationJournal: Protein Sci. / Year: 1998
Title: Structure and stability of the P93G variant of ribonuclease A.
Authors: Schultz, L.W. / Hargraves, S.R. / Klink, T.A. / Raines, R.T.
History
DepositionOct 20, 1997Processing site: BNL
Revision 1.0Apr 22, 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
Revision 1.5Oct 30, 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 A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7393
Polymers13,6681
Non-polymers712
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.790, 65.790, 66.120
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


Mass: 13668.264 Da / Num. of mol.: 1 / Mutation: P93G
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: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 129 / 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: 3.02 Å3/Da / Density % sol: 60 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: 6UL DROPS COMPOSED OF 15MG/ML PROTEIN,50MM SODIUM ACETATE AT PH 6.0, 15% SATURATED AMMONIUM SULFATE AND 25% SATURATED SODIUM CHLORIDE WERE SUSPENDED OVER 0.5ML WELLS CONTAINING 100MM SODIUM ...Details: 6UL DROPS COMPOSED OF 15MG/ML PROTEIN,50MM SODIUM ACETATE AT PH 6.0, 15% SATURATED AMMONIUM SULFATE AND 25% SATURATED SODIUM CHLORIDE WERE SUSPENDED OVER 0.5ML WELLS CONTAINING 100MM SODIUM ACETATE, PH 6.0, 30% SATURATED AMMONIUM SULFATE AND 50% SATURATED SODIUM CHLORIDE. TEMPERATURE: 20C., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMsodium acetate1drop
215 mg/mlprotein1drop
315 %(v/v)satammonium sulfate1drop
425 %(v/v)sat1dropNaCl
5100 mMsodium acetate1reservoir
630 %(v/v)satammonium sulfate1reservoir
750 %(v/v)sat1reservoirNaCl

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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: Apr 11, 1997 / Details: LONG MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 22780 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.028 / Rsym value: 0.028 / Net I/σ(I): 20
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 3 / Rsym value: 0.15 / % possible all: 93

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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: 1.7→30 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: THE FOLLOWING RESIDUES WERE MODELED WITH TWO CONFORMATIONS: THR 17, ASN 24, SER 59, ASP 83. ASP 83 MAKES A WATER MEDIATED HYDROGEN BOND VIA HOH 183 WITH OG1 OF THR 45 AND MAKES A DIRECT ...Details: THE FOLLOWING RESIDUES WERE MODELED WITH TWO CONFORMATIONS: THR 17, ASN 24, SER 59, ASP 83. ASP 83 MAKES A WATER MEDIATED HYDROGEN BOND VIA HOH 183 WITH OG1 OF THR 45 AND MAKES A DIRECT HYDROGEN BOND TO OG1 OF THR 45 IN THE B POSITION.
RfactorNum. reflection% reflection
Rwork0.17 --
all-18621 -
obs-18621 93 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 221 Å2 / ksol: 0.82 e/Å3
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 2 129 1108
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01110048
X-RAY DIFFRACTIONt_angle_deg2.50413637
X-RAY DIFFRACTIONt_dihedral_angle_d17.5796230
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0053025
X-RAY DIFFRACTIONt_gen_planes0.0114850
X-RAY DIFFRACTIONt_it1
X-RAY DIFFRACTIONt_nbd0.034750
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.00525
X-RAY DIFFRACTIONt_plane_restr0.0150

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