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- PDB-5rat: Effects of temperature on protein structure and dynamics: X-ray c... -

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Basic information

Entry
Database: PDB / ID: 5rat
TitleEffects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 TO 320 K
ComponentsRIBONUCLEASE APancreatic ribonuclease family
KeywordsHYDROLASE (NUCLEIC ACID / RNA)
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: 1.5 Å
AuthorsTiltonjunior, R.F. / Dewan, J.C. / Petsko, G.A.
Citation
Journal: Biochemistry / Year: 1992
Title: Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K.
Authors: Tilton Jr., R.F. / Dewan, J.C. / Petsko, G.A.
#1: Journal: J.Appl.Crystallogr. / Year: 1987
Title: Greatly Reduced Radiation Damage in Ribonuclease Crystals Mounted on Glass Fibers
Authors: Dewan, J.C. / Tilton, R.F.
History
DepositionAug 13, 1991-
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)13,7081
Polymers13,7081
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.140, 38.230, 53.160
Angle α, β, γ (deg.)90.00, 106.96, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO 93 AND PRO 114 ARE CIS-PROLINES.

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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 genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.5 / Method: batch method
Details: taken from Gilbert, W.A. et al. (1982) J. Raman. Spectrosc., 12, 173-179.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein11
20.2 M11NaOH
350 %(v/v)methanol11

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Data collection

DiffractionMean temperature: 220 K
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 10235 / Observed criterion σ(I): 2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.5 Å / σ(I): 2 /
RfactorNum. reflection
obs0.151 10235
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 0 0 951
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.03
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0160.025
X-RAY DIFFRACTIONp_chiral_restr0.1460.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.35
X-RAY DIFFRACTIONp_staggered_tor16.215
X-RAY DIFFRACTIONp_orthonormal_tor17.615
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.5 Å / Num. reflection obs: 10235 / Rfactor obs: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS

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