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- PDB-4i65: Crystal Structure of Staphylococcal nuclease mutant V23I/L25V/I72... -

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Basic information

Entry
Database: PDB / ID: 4i65
TitleCrystal Structure of Staphylococcal nuclease mutant V23I/L25V/I72V/I92V
ComponentsThermonuclease
KeywordsHYDROLASE
Function / homology
Function and homology information


: / micrococcal nuclease / nucleic acid binding / extracellular region / metal ion binding / membrane
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / 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) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / 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: 1.61 Å
AuthorsWeir, D.M. / Janowska, K. / Sakon, J. / Stites, W.E.
CitationJournal: To be Published
Title: Hydrophobic core mutants of Staphylococcal nuclease
Authors: Weir, D.M. / Janowska, K. / Sakon, J. / Stites, W.E.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Thermonuclease


Theoretical massNumber of molelcules
Total (without water)15,5091
Polymers15,5091
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.980, 47.980, 63.590
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 Thermonuclease / TNase / Micrococcal nuclease / Staphylococcal nuclease


Mass: 15509.003 Da / Num. of mol.: 1 / Fragment: UNP Residues 83-223 / Mutation: V23I, L25V, I72V, 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


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25mM Sodium Phosphate buffer, 35-60% MPD, Vapor Diffusion, Hanging Drop, Temperature 277K, pH 7.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Apr 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→15.08 Å / Num. all: 30601 / Num. obs: 14804 / % possible obs: 78.3 % / Observed criterion σ(I): 9.5
Reflection shellResolution: 1.6→1.66 Å / % possible all: 12.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CCP4model building
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→14.76 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.219 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23911 767 5.2 %RANDOM
Rwork0.19003 ---
obs0.19254 14023 79.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.319 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.61→14.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 0 75 1164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221140
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9791528
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0724.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05715236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.604156
X-RAY DIFFRACTIONr_chiral_restr0.110.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02825
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.2458
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.2764
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.290.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.742698
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.78631098
X-RAY DIFFRACTIONr_scbond_it3.4013.5502
X-RAY DIFFRACTIONr_scangle_it5.2984.5430
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.651 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 10 -
Rwork0.382 153 -
obs--11.89 %

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