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- PDB-1bel: HYDROLASE PHOSPHORIC DIESTER, RNA -

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Basic information

Entry
Database: PDB / ID: 1bel
TitleHYDROLASE PHOSPHORIC DIESTER, RNA
ComponentsRIBONUCLEASE APancreatic ribonuclease family
KeywordsHYDROLASE / HYDROLASE (PHOSPHORIC DIESTER / RNA) / NUCLEASE / ENDONUCLEASE / 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
METHANOL / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDung, M.H. / Bell, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Structure of crystal form IX of bovine pancreatic ribonuclease A.
Authors: Dung, M.H. / Bell, J.A.
History
DepositionDec 21, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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

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Assembly

Deposited unit
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0297
Polymers13,7081
Non-polymers3206
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.900, 44.800, 52.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RIBONUCLEASE A / Pancreatic ribonuclease family


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PH 4.5 / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MOH / METHANOL / Methanol


Mass: 32.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH4O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 4

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 30 %
Crystal growpH: 4.5 / Details: 60% METHANOL, pH 4.50
Crystal
*PLUS
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein11
258 %(v/v)methanol11

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 28, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→10 Å / Num. obs: 12318 / % possible obs: 82 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 6.36
Reflection shellResolution: 1.6→1.8 Å / Mean I/σ(I) obs: 4.22 / % possible all: 61
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. measured all: 76694
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.8 Å

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Processing

Software
NameClassification
bioteXdata collection
bioteXdata reduction
MERLOTphasing
TNTrefinement
bioteXdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RN3

3rn3


Resolution: 1.6→10 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: FINAL B VALUES CALCULATED BY GRADIENT METHOD
RfactorNum. reflection% reflection
all0.15 12318 -
obs0.15 12318 82 %
Solvent computationSolvent model: BABINET / Bsol: 117 Å2 / ksol: 0.57 e/Å3
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 10 90 1051
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.019831
X-RAY DIFFRACTIONt_angle_deg1.92513211.5
X-RAY DIFFRACTIONt_dihedral_angle_d0
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle0
X-RAY DIFFRACTIONt_trig_c_planes0.01281.5
X-RAY DIFFRACTIONt_gen_planes0.0161404
X-RAY DIFFRACTIONt_it0
X-RAY DIFFRACTIONt_nbd0.008420
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.011.5
X-RAY DIFFRACTIONt_plane_restr0.0164
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.68 Å / Rfactor obs: 0.233

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