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- PDB-3rn3: SEGMENTED ANISOTROPIC REFINEMENT OF BOVINE RIBONUCLEASE A BY THE ... -

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Basic information

Entry
Database: PDB / ID: 3rn3
TitleSEGMENTED ANISOTROPIC REFINEMENT OF BOVINE RIBONUCLEASE A BY THE APPLICATION OF THE RIGID-BODY TLS MODEL
ComponentsRIBONUCLEASE A
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: 1.45 Å
AuthorsHowlin, B. / Moss, D.S. / Harris, G.W. / Palmer, R.A.
Citation
Journal: Acta Crystallogr.,Sect.A / Year: 1989
Title: Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model.
Authors: Howlin, B. / Moss, D.S. / Harris, G.W.
#1: Journal: Biochim.Biophys.Acta / Year: 1987
Title: Ribonuclease A. Analysis of the Hydrogen Bond Geometry, and Spatial Accessibility at the Active Site
Authors: Harris, G.W. / Borkakoti, N. / Moss, D.S. / Palmer, R.A. / Howlin, B.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1986
Title: Comparison of Two Independently Refined Models of Ribonuclease-A
Authors: Wlodawer, A. / Borkakoti, N. / Moss, D.S. / Howlin, B.
#3: Journal: J.Crystallogr.Spectrosc.Res. / Year: 1984
Title: The Refined Structure of Ribonuclease-A at 1.45 Angstroms Resolution
Authors: Borkakoti, N. / Moss, D.S. / Stanford, M.J. / Palmer, R.A.
#4: Journal: J.Mol.Biol. / Year: 1983
Title: Specificity of Pancreatic Ribonuclease-A. An X-Ray Study of a Protein-Nucleotide Complex
Authors: Borkakoti, N. / Palmer, R.A. / Haneef, I. / Moss, D.S.
#5: Journal: Eur.J.Biochem. / Year: 1983
Title: The Active Site of Ribonuclease A from the Crystallographic Studies of Ribonuclease-A-Inhibitor Complexes
Authors: Borkakoti, N.
#6: Journal: Acta Crystallogr.,Sect.B / Year: 1982
Title: Ribonuclease-A. Least-Squares Refinement of the Structure at 1.45 Angstroms Resolution
Authors: Borkakoti, N. / Moss, D.S. / Palmer, R.A.
#7: Journal: J.Mol.Biol. / Year: 1974
Title: The Structure of Ribonuclease At 2.5 Angstrom Resolution
Authors: Carlisle, C.H. / Palmer, R.A. / Mazumdar, S.K. / Gorinsky, B.A. / Yeates, D.G.R.
History
SupersessionOct 15, 1991ID: 1RN3
DepositionOct 30, 1991Processing site: BNL
Revision 1.0Oct 31, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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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)13,8042
Polymers13,7081
Non-polymers961
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.450, 38.369, 53.215
Angle α, β, γ (deg.)90.00, 105.96, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES 93 AND 114 ARE CIS-PROLINES. / 2: SEE REMARK 5.

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Components

#1: Protein RIBONUCLEASE 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 / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Compound detailsA SECOND SITE HAS BEEN LOCATED AND REFINED FOR HIS 119.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.57 %

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementHighest resolution: 1.45 Å
Details: THE CARBOXAMIDE TERMINI OF RESIDUES ASN 24, ASN 27, ASN 67, GLN 69, ASN 71, GLN 74, ASN 94, AND ASN 103 WERE "FLIPPED" BY 180 DEGREES TO CONFORM TO THE ASSIGNMENT OBSERVED IN THE STRUCTURE ...Details: THE CARBOXAMIDE TERMINI OF RESIDUES ASN 24, ASN 27, ASN 67, GLN 69, ASN 71, GLN 74, ASN 94, AND ASN 103 WERE "FLIPPED" BY 180 DEGREES TO CONFORM TO THE ASSIGNMENT OBSERVED IN THE STRUCTURE DEPOSITED BY WLODAWER ET AL (ENTRY 7RSA).
RfactorNum. reflection
obs0.2233 19238
Refinement stepCycle: LAST / Highest resolution: 1.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 5 107 1069
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.15
X-RAY DIFFRACTIONp_angle_d0.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.45 Å / Num. reflection obs: 19238 / Rfactor obs: 0.2233
Solvent computation
*PLUS
Displacement parameters
*PLUS

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