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- PDB-1bnf: BARNASE T70C/S92C DISULFIDE MUTANT -

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Basic information

Entry
Database: PDB / ID: 1bnf
TitleBARNASE T70C/S92C 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 / 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 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
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)37,2503
Polymers37,2503
Non-polymers00
Water4,107228
1
A: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,4171
Polymers12,4171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,4171
Polymers12,4171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,4171
Polymers12,4171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.140, 59.140, 81.790
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: 12416.825 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.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 44.5 %
Crystal
*PLUS
Density % sol: 37.3 %
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 sourceSource: SYNCHROTRON / Site: SRS / Type: SRS
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: 1993
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 20982 / % possible obs: 97.2 % / Observed criterion σ(I): 3 / Redundancy: 2.41 % / Rmerge(I) obs: 0.122
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10.3 Å / Num. measured all: 50660 / Rmerge(I) obs: 0.122

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Processing

Software
NameClassification
MOSFLMdata reduction
PROLSQrefinement
RefinementResolution: 2→6 Å / σ(F): 0
Details: SSBOND THERE IS TWO-FOLD DISORDER IN THE ENGINEERED DISULFIDE BOND IN ALL THREE CHAINS, A, B, AND C.
RfactorNum. reflection
obs0.173 50660
Displacement parametersBiso mean: 13.5 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 0 228 2771
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0420.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9491.5
X-RAY DIFFRACTIONp_mcangle_it1.4532
X-RAY DIFFRACTIONp_scbond_it1.8262
X-RAY DIFFRACTIONp_scangle_it2.5413
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1190.12
X-RAY DIFFRACTIONp_singtor_nbd0.1510.2
X-RAY DIFFRACTIONp_multtor_nbd0.1490.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1380.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.1393
X-RAY DIFFRACTIONp_staggered_tor15.21920
X-RAY DIFFRACTIONp_orthonormal_tor18.89815
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 20982
Solvent computation
*PLUS
Displacement parameters
*PLUS

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