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- PDB-2f0d: Crystal structure of Staphylococcal nuclease mutant I92V -

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Basic information

Entry
Database: PDB / ID: 2f0d
TitleCrystal structure of Staphylococcal nuclease mutant I92V
ComponentsStaphylococcal nucleaseMicrococcal nuclease
KeywordsHYDROLASE / DNA HYDROLASE / RNA HYDROLASE / ENDONUCLEASE / CALCIUM / SIGNAL
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLu, J.Z. / Sakon, J. / Stites, W.E.
CitationJournal: To be Published
Title: Hydrophobic core mutants of Staphylococcal nuclease
Authors: Lu, J.Z. / Sakon, J. / Stites, W.E.
History
DepositionNov 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 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)16,8291
Polymers16,8291
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.200, 48.200, 63.700
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 / E.C.3.1.31.1 / Thermonuclease / TNase / Micrococcal nuclease


Mass: 16829.303 Da / Num. of mol.: 1 / Mutation: I92V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: pL13 / Production host: Escherichia coli (E. coli) / Strain (production host): AR120 / References: UniProt: P00644, micrococcal nuclease
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM phosphate buffer, 45% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 5099 / Num. obs: 4786 / % possible obs: 93.9 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CNS1.1refinement
XTALVIEWrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.1619 256 5 %
Rwork0.1683 --
all0.16831 5099 -
obs0.16831 4786 93.9 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.543 Å20 Å20 Å2
2---3.543 Å20 Å2
3---7.085 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 0 12 1102
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006199
X-RAY DIFFRACTIONc_angle_deg1.23817
X-RAY DIFFRACTIONc_mcbond_it1.4681.5
X-RAY DIFFRACTIONc_mcangle_it2.5062
X-RAY DIFFRACTIONc_scbond_it2.3132
X-RAY DIFFRACTIONc_scangle_it3.6072.5

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