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- PDB-1bni: BARNASE WILDTYPE STRUCTURE AT PH 6.0 -

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Basic information

Entry
Database: PDB / ID: 1bni
TitleBARNASE WILDTYPE STRUCTURE AT PH 6.0
ComponentsBARNASE
KeywordsMICROBIAL RIBONUCLEASE / ALPHA/BETA PROTEIN
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 / SYNCHROTRON / Resolution: 2.1 Å
AuthorsCameron, A. / Henrick, K. / Fersht, A.R. / Dodson, G. / Buckle, A.M.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Crystal structural analysis of mutations in the hydrophobic cores of barnase.
Authors: Buckle, A.M. / Henrick, K. / Fersht, A.R.
#1: Journal: Nature / Year: 1982
Title: Molecular Structure 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
DepositionMay 17, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: BARNASE
B: BARNASE
C: BARNASE


Theoretical massNumber of molelcules
Total (without water)37,1963
Polymers37,1963
Non-polymers00
Water3,891216
1
A: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,3991
Polymers12,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,3991
Polymers12,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,3991
Polymers12,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.390, 59.390, 82.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein BARNASE


Mass: 12398.721 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Plasmid: PUC19 / Production host: Escherichia coli (E. coli)
References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
145 %satammonium sulfate1reservoir
23.0 Mammonium phosphate1reservoir
30.02 Mzinc sulphate1reservoir
410-20 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorDetector: FILM
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. obs: 16312 / % possible obs: 80 % / Observed criterion σ(I): 3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.089
Reflection
*PLUS
Rmerge(I) obs: 0.089

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Processing

Software
NameClassification
PROLSQrefinement
MOSFLMdata reduction
RefinementResolution: 2.1→10 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.179 16312 80 %
Displacement parametersBiso mean: 15.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2547 0 0 216 2763
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0580.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0660.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9991
X-RAY DIFFRACTIONp_mcangle_it1.7711.5
X-RAY DIFFRACTIONp_scbond_it1.7031.5
X-RAY DIFFRACTIONp_scangle_it2.5292
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.1460.12
X-RAY DIFFRACTIONp_singtor_nbd0.1960.5
X-RAY DIFFRACTIONp_multtor_nbd0.2260.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2260.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.23.2
X-RAY DIFFRACTIONp_staggered_tor18.918.9
X-RAY DIFFRACTIONp_orthonormal_tor22.922.9
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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