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- PDB-1bne: BARNASE A43C/S80C DISULFIDE MUTANT -

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Basic information

Entry
Database: PDB / ID: 1bne
TitleBARNASE A43C/S80C DISULFIDE MUTANT
ComponentsBARNASE
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 / Guanine-specific ribonuclease N1/T1/U2 / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsClarke, J. / Henrick, K. / Fersht, A.R.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Disulfide mutants of barnase. I: Changes in stability and structure assessed by biophysical methods and X-ray crystallography.
Authors: Clarke, J. / Henrick, K. / Fersht, A.R.
History
DepositionMar 31, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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: BARNASE
B: BARNASE
C: BARNASE


Theoretical massNumber of molelcules
Total (without water)37,3413
Polymers37,3413
Non-polymers00
Water4,143230
1
A: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,4471
Polymers12,4471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,4471
Polymers12,4471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,4471
Polymers12,4471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.600, 59.600, 81.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Atom site foot note1: THR A 79 - CYS A 80 OMEGA = 215.73 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein BARNASE


Mass: 12446.852 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: BARNASE / Plasmid: PTZ18 DERIVED / Gene (production host): BARNASE / 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.: 230 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal
*PLUS
Density % sol: 38.2 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-20 mg/mlprotein1drop
210 mM1dropNa2HPO4
325 mMTris-HCl1drop
41 mMEDTA1drop
51 mMdithiothreitol1drop
635-40 %PEG80001reservoir
750 mMsodium acetate1reservoir
850 mMsodium cacodylate1reservoir
95 mMsodium phosphate1reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: 1993
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 16295 / % possible obs: 85.9 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.131
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 13.5 Å / Num. measured all: 57655 / Rmerge(I) obs: 0.131

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Processing

Software
NameClassification
MOSFLMdata reduction
PROLSQrefinement
RefinementResolution: 2.1→6 Å / σ(F): 0 /
RfactorNum. reflection
obs0.169 57655
Displacement parametersBiso mean: 16.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 0 230 2770
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8171.5
X-RAY DIFFRACTIONp_mcangle_it1.32
X-RAY DIFFRACTIONp_scbond_it1.5583
X-RAY DIFFRACTIONp_scangle_it2.1863
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1170.12
X-RAY DIFFRACTIONp_singtor_nbd0.1510.2
X-RAY DIFFRACTIONp_multtor_nbd0.1450.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1480.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.9233
X-RAY DIFFRACTIONp_staggered_tor16.36420
X-RAY DIFFRACTIONp_orthonormal_tor20.39315
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 16295
Solvent computation
*PLUS
Displacement parameters
*PLUS

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