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- PDB-1rnw: RECOMBINANT RIBONUCLEASE A CRYSTALLIZED FROM 80% AMMONIUM SULPHATE -

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Basic information

Entry
Database: PDB / ID: 1rnw
TitleRECOMBINANT RIBONUCLEASE A CRYSTALLIZED FROM 80% AMMONIUM SULPHATE
ComponentsRIBONUCLEASE A
KeywordsENDONUCLEASE / HYDROLASE / NUCLEASE / GLYCOPROTEIN
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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsFedorov, A.A. / Joseph-Mccarthy, D. / Fedorov, E.V. / Sirakova, D. / Graf, I. / Almo, S.C.
CitationJournal: Biochemistry / Year: 1996
Title: Ionic interactions in crystalline bovine pancreatic ribonuclease A.
Authors: Fedorov, A.A. / Joseph-McCarthy, D. / Fedorov, E. / Sirakova, D. / Graf, I. / Almo, S.C.
History
DepositionNov 8, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)13,9003
Polymers13,7081
Non-polymers1922
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.609, 64.609, 65.191
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 / RNASE A


Mass: 13708.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: PANCREAS / Production host: Escherichia coli (E. coli) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.87 Å3/Da / Density % sol: 57 %
Crystal growpH: 5.5 / Details: CRYSTALLIZED FROM 80% AMMONIUM SULFATE, pH 5.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mg/mlprotein1drop
230 %ammonium sulfate1reservoir
33.0 M1reservoirCsCl
40.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→28.9 Å / Num. obs: 13874 / % possible obs: 92.6 % / Redundancy: 2.89 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 20.17

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Processing

Software
NameClassification
XDSdata scaling
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 1.8→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.167 --
obs-12877 87.1 %
Displacement parametersBiso mean: 23.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 10 110 1071
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.018
X-RAY DIFFRACTIONp_angle_d0.030.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.381.5
X-RAY DIFFRACTIONp_mcangle_it2.352
X-RAY DIFFRACTIONp_scbond_it2.712
X-RAY DIFFRACTIONp_scangle_it4.373
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1360.15
X-RAY DIFFRACTIONp_singtor_nbd0.1720.3
X-RAY DIFFRACTIONp_multtor_nbd0.1760.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2040.3
X-RAY DIFFRACTIONp_planar_tor1.82
X-RAY DIFFRACTIONp_staggered_tor15.910
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor19.910
X-RAY DIFFRACTIONp_special_tor
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS

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