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- PDB-1izp: F46L mutant of bovine pancreatic ribonuclease A -

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Basic information

Entry
Database: PDB / ID: 1izp
TitleF46L mutant of bovine pancreatic ribonuclease A
ComponentsRIBONUCLEASE APancreatic ribonuclease family
KeywordsHYDROLASE / RIBONUCLEASE / RNASE A / BOVINE PANCREAS
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 / SYNCHROTRON / Resolution: 1.5 Å
AuthorsKadonosono, T. / Chatani, E. / Hayashi, R. / Moriyama, H. / Ueki, T.
CitationJournal: Biochemistry / Year: 2003
Title: Minimization of cavity size ensures protein stability and folding: structures of Phe46-replaced bovine pancreatic RNase A
Authors: Kadonosono, T. / Chatani, E. / Hayashi, R. / Moriyama, H. / Ueki, T.
History
DepositionOct 11, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE A


Theoretical massNumber of molelcules
Total (without water)13,6741
Polymers13,6741
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.983, 63.983, 63.482
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a monomer

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Components

#1: Protein RIBONUCLEASE A / Pancreatic ribonuclease family / Ribonuclease pancreatic


Mass: 13674.311 Da / Num. of mol.: 1 / Mutation: F46L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Tissue: pancreas / Plasmid: pETRN / Production host: Escherichia coli (E. coli) / References: UniProt: P61823, EC: 3.1.27.5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.32 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, sodium chloride, sodium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.0
21 mMEDTA1drop
3100 mMsodium acetate1reservoirpH6.0
41.5 Mammonium sulfate1reservoir
52 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2000
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 24330 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 9 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 9 % / Rmerge(I) obs: 0.191 / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 24356 / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 1.5→6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 696851.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2226 9.9 %RANDOM
Rwork0.199 ---
obs0.199 22522 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 117.628 Å2 / ksol: 0.866345 e/Å3
Displacement parametersBiso mean: 15.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.73 Å20 Å2
2--0.67 Å20 Å2
3----1.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.05 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms948 0 0 206 1154
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.222 356 10.2 %
Rwork0.186 3119 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Rfactor Rfree: 0.23 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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