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- PDB-4rsk: STRUCTURE OF THE K7A/R10A/K66A VARIANT OF RIBONUCLEASE A COMPLEXE... -

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Basic information

Entry
Database: PDB / ID: 4rsk
TitleSTRUCTURE OF THE K7A/R10A/K66A VARIANT OF RIBONUCLEASE A COMPLEXED WITH 3'-UMP
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
3'-URIDINEMONOPHOSPHATE / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.1 Å
AuthorsSchultz, L.W. / Fisher, B.M. / Raines, R.T.
CitationJournal: Biochemistry / Year: 1998
Title: Coulombic Effects of Remote Subsites on the Active Site of Ribonuclease A
Authors: Fisher, B.M. / Schultz, L.W. / Raines, R.T.
History
DepositionApr 9, 1998Processing site: BNL
Revision 1.0Dec 9, 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 23, 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)13,8302
Polymers13,5061
Non-polymers3241
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.620, 69.620, 66.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-264-

HOH

21A-275-

HOH

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Components

#1: Protein RIBONUCLEASE A


Mass: 13506.006 Da / Num. of mol.: 1 / Mutation: K7A, R10A, K66A
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-U3P / 3'-URIDINEMONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.47 Å3/Da / Density % sol: 60 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5
Details: CRYSTALS WERE PREPARED USING THE HANGING DROP METHOD. LYOPHILIZED K7A/R10A/K66A RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ML. DROPS CONSISTING OF PROTEIN SOLUTION ...Details: CRYSTALS WERE PREPARED USING THE HANGING DROP METHOD. LYOPHILIZED K7A/R10A/K66A RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ML. DROPS CONSISTING OF PROTEIN SOLUTION (1.5MICROLITER), WATER (1.5MICROLITER), AND RESERVOIR SOLUTION (3.0MICROLITER) WERE SUSPENDED OVER 0.5 ML OF RESERVOIR SOLUTION (0.1M SODIUM ACETATE BUFFER, PH 4.5, CONTAINING 36% PEG 4000). THE COMPLEX WITH 3'-UMP WAS PREPARED BY SOAKING CRYSTALS IN MOTHER LIQUOR CONTAINING 5MM 3'-UMP FOR 2 DAYS., 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-IDDetails
160 mg/mlprotein1drop
30.1 Msodium acetate1reservoir
436 %(w/v)PEG40001reservoir
2water1drop0.0015mM

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 12, 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: 2.1→30 Å / Num. obs: 33552 / % possible obs: 88 % / Observed criterion σ(I): 0.33 / Redundancy: 2.4 % / Rsym value: 0.026 / Net I/σ(I): 19.8
Reflection shellResolution: 2.1→2.2 Å / Rsym value: 0.12 / % possible all: 88
Reflection
*PLUS
Num. obs: 14210 / Num. measured all: 33552 / Rmerge(I) obs: 0.026
Reflection shell
*PLUS
% possible obs: 88 % / Rmerge(I) obs: 0.122

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Processing

Software
NameClassification
XDSdata scaling
XCALIBREdata reduction
TNTrefinement
XDSdata reduction
XCALIBREdata scaling
TNTphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 3RSK

3rsk


Resolution: 2.1→30 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.168 14210 -
obs-14210 88 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 135 Å2 / ksol: 0.56 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 21 94 1052
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0119838
X-RAY DIFFRACTIONt_angle_deg2.208133412
X-RAY DIFFRACTIONt_dihedral_angle_d17.4755890
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0062825
X-RAY DIFFRACTIONt_gen_planes0.01114050
X-RAY DIFFRACTIONt_it1
X-RAY DIFFRACTIONt_nbd0.018650
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_deg17.4750
X-RAY DIFFRACTIONt_planar_d0.00625
X-RAY DIFFRACTIONt_plane_restr0.01150

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