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- PDB-1snq: PROTEIN STABILITY IN STAPHYLOCOCCAL NUCLEASE -

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Basic information

Entry
Database: PDB / ID: 1snq
TitlePROTEIN STABILITY IN STAPHYLOCOCCAL NUCLEASE
ComponentsSTAPHYLOCOCCAL NUCLEASEMicrococcal nuclease
KeywordsHYDROLASE / NUCLEASE / ENDONUCLEASE / CALCIUM
Function / homology
Function and homology information


endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / membrane / metal ion binding
Similarity search - Function
Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsTruckses, D.M. / Somoza, J.R. / Markley, J.L.
Citation
Journal: Protein Sci. / Year: 1996
Title: Coupling between trans/cis proline isomerization and protein stability in staphylococcal nuclease.
Authors: Truckses, D.M. / Somoza, J.R. / Prehoda, K.E. / Miller, S.C. / Markley, J.L.
#1: Journal: Biochemistry / Year: 1994
Title: Engineering Alternative Beta-Turn Types in Staphylococcal Nuclease
Authors: Hynes, T.R. / Hodel, A. / Fox, R.O.
#2: Journal: Proteins / Year: 1991
Title: The Crystal Structure of Staphylococcal Nuclease Refined at 1.7 A Resolution
Authors: Hynes, T.R. / Fox, R.O.
#3: Journal: Biochemistry / Year: 1990
Title: Coupling between Local Structure and Global Stability of a Protein: Mutants of Staphylococcal Nuclease
Authors: Alexandrescu, A.T. / Hinck, A.P. / Markley, J.L.
History
DepositionJul 6, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STAPHYLOCOCCAL NUCLEASE


Theoretical massNumber of molelcules
Total (without water)16,7381
Polymers16,7381
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.180, 49.180, 63.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein STAPHYLOCOCCAL NUCLEASE / Micrococcal nuclease / MICROCOCCAL NUCLEASE


Mass: 16738.215 Da / Num. of mol.: 1 / Mutation: P47G, P117G
Source method: isolated from a genetically manipulated source
Details: THIS STAPH NUCLEASE IS FROM THE V8 STRAIN, THEREFORE RESIDUE 124 IS LEU, NOT HIS AS IN THE FOGGI STRAIN
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: V8 / Description: PET SYSTEM / Gene: NUC / Plasmid: PET3A / Gene (production host): NUC / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: P00644, micrococcal nuclease
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growpH: 8.15
Details: 10.5 MM POTASSIUM PHOSPHATE, 20% - 30% 2-METHYL-2,4-PENTANEDIOL, pH 8.15
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Details: Loll, P.J., (1989) Proteins: Struct.,Funct., Genet., 5, 183.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mldrop1drop
210.5 mMpotassium phosphate1drop
317 %(w/w)MPD1drop
410 mM1dropCaCl2
520 mMpotassium citrate1drop
610.5 mMpotassium phosphate1reservoir
720-30 %(w/w)MPD1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 10604 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0474
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 9999 Å / Num. measured all: 30773
Reflection shell
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 2 Å / % possible obs: 90 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing
RefinementResolution: 1.7→6 Å / σ(F): 2
RfactorNum. reflection
Rfree0.274 -
Rwork0.187 -
obs0.187 10604
Displacement parametersBiso mean: 49.9 Å2
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 0 0 25 1064
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 10604 / Num. reflection obs: 9523 / Highest resolution: 1.95 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.602
X-RAY DIFFRACTIONx_dihedral_angle_deg24.112
X-RAY DIFFRACTIONx_improper_angle_deg1.38

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