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- PDB-1brn: SUBSITE BINDING IN AN RNASE: STRUCTURE OF A BARNASE-TETRANUCLEOTI... -

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Basic information

Entry
Database: PDB / ID: 1brn
TitleSUBSITE BINDING IN AN RNASE: STRUCTURE OF A BARNASE-TETRANUCLEOTIDE COMPLEX AT 1.76 ANGSTROMS RESOLUTION
Components
  • DNA (5'-D(*CP*GP*AP*C)-3')
  • PROTEIN (BARNASE (E.C.3.1.27.-))
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / HYDROLASE-DNA COMPLEX
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: 1.76 Å
AuthorsBuckle, A.M. / Fersht, A.R.
Citation
Journal: Biochemistry / Year: 1994
Title: Subsite binding in an RNase: structure of a barnase-tetranucleotide complex at 1.76-A resolution.
Authors: Buckle, A.M. / Fersht, A.R.
#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
DepositionNov 17, 1993Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*AP*C)-3')
B: DNA (5'-D(*CP*GP*AP*C)-3')
L: PROTEIN (BARNASE (E.C.3.1.27.-))
M: PROTEIN (BARNASE (E.C.3.1.27.-))


Theoretical massNumber of molelcules
Total (without water)27,1494
Polymers27,1494
Non-polymers00
Water4,125229
1
A: DNA (5'-D(*CP*GP*AP*C)-3')
L: PROTEIN (BARNASE (E.C.3.1.27.-))


Theoretical massNumber of molelcules
Total (without water)13,5752
Polymers13,5752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (5'-D(*CP*GP*AP*C)-3')
M: PROTEIN (BARNASE (E.C.3.1.27.-))


Theoretical massNumber of molelcules
Total (without water)13,5752
Polymers13,5752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.866, 54.286, 29.607
Angle α, β, γ (deg.)107.77, 89.05, 96.37
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 1175.819 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (BARNASE (E.C.3.1.27.-))


Mass: 12398.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal grow
*PLUS
Method: other / Details: NMR

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.76 Å / Num. obs: 18358 / % possible obs: 78 % / Num. measured all: 34544 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 83.8 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 23.2

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.19 / Rfactor obs: 0.19 / Highest resolution: 1.76 Å
Details: ONLY ATOM O3' OF THE 5'-TERMINAL END RESIDUES C A 1 AND C B 1 ARE VISIBLE IN THE ELECTRON DENSITY MAPS.
Refinement stepCycle: LAST / Highest resolution: 1.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 126 0 229 2083
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.92
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.76 Å / Lowest resolution: 6 Å / Num. reflection obs: 2048 / σ(F): 1 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.92

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