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- PDB-1rnb: CRYSTAL STRUCTURE OF A BARNASE-D(*GP*C) COMPLEX AT 1.9 ANGSTROMS ... -

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Basic information

Entry
Database: PDB / ID: 1rnb
TitleCRYSTAL STRUCTURE OF A BARNASE-D(*GP*C) COMPLEX AT 1.9 ANGSTROMS RESOLUTION
Components
  • BARNASE
  • DNA (5'-D(*GP*C)-3')
KeywordsENDONUCLEASE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region
Similarity search - Function
: / Barnase / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsJanin, J. / Baudet, S.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Crystal structure of a barnase-d(GpC) complex at 1.9 A resolution.
Authors: Baudet, S. / Janin, J.
#1: Journal: Nature / Year: 1982
Title: Molecular Structures of a New Family of Ribonucleases
Authors: Mauguen, Y. / Hartley, R.W. / Dodson, E.J. / Dodson, G.G. / Bricogne, G. / Chothia, C. / Jack, A.
History
DepositionMar 19, 1991Processing site: NDB
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _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
C: DNA (5'-D(*GP*C)-3')
A: BARNASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0683
Polymers12,9722
Non-polymers961
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.970, 57.970, 85.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: THE SIDE CHAINS OF RESIDUES 2, 59, 60, AND 62 HAVE NO DENSITY.

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Components

#1: DNA chain DNA (5'-D(*GP*C)-3')


Mass: 573.430 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Protein BARNASE


Mass: 12398.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / References: UniProt: P00648
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.0 Mammonium sulfate1drop
20.7 mMBarnase1reservoir
33.5 mMd(GpC)1reservoir
41.5 Mammonium sulphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 12204 / Num. measured all: 26792 / Rmerge(I) obs: 0.058

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor Rwork: 0.214 / Highest resolution: 1.9 Å
Details: THE DINUCLEOTIDE IS BOUND IN NON-PRODUCTIVE MODE AND IS INVOLVED IN CRYSTAL CONTACTS. THE SIDE CHAINS OF RESIDUES 2, 59, 60, AND 62 HAVE NO DENSITY.
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms869 38 5 96 1008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.019
X-RAY DIFFRACTIONo_angle_d0.059
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5.5 Å / Num. reflection all: 10578 / Num. reflection obs: 9679 / σ(F): 3 / Rfactor obs: 0.214 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.05
X-RAY DIFFRACTIONp_dihedral_angle_d0.050.061
X-RAY DIFFRACTIONp_plane_restr0.020.014
X-RAY DIFFRACTIONp_chiral_restr0.150.221

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