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- PDB-4k8i: Crystal Structure of Staphylococcal Nuclease mutant I92V/V99L -

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Basic information

Entry
Database: PDB / ID: 4k8i
TitleCrystal Structure of Staphylococcal Nuclease mutant I92V/V99L
ComponentsThermonuclease
KeywordsHYDROLASE / DNA hydrolase / RNA hydrolase / endonuclease
Function / homology
Function and homology information


3' overhang single-stranded DNA endodeoxyribonuclease activity / 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: 2.1 Å
AuthorsSanders, J.M. / Latimer, E.C. / Roeser, J.R. / Janowska, K. / Sakon, J. / Stites, W.E.
CitationJournal: To be Published
Title: Hydrophobic core mutants of Staphylococcal nuclease
Authors: Sanders, J.M. / Latimer, E.C. / Roeser, J.R. / Janowska, K. / Sakon, J. / Stites, W.E.
History
DepositionApr 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 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)15,4081
Polymers15,4081
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.200, 47.200, 63.400
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 / Nuclease B / Nuclease A


Mass: 15407.873 Da / Num. of mol.: 1 / Fragment: UNP Residues 89-223 / Mutation: I174V/V191L
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.: 40 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25mM Sodium Phosphate, MPD 35-60%, pH 7.0, 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 SATURN 92 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.59→22.13 Å / Num. obs: 26865 / Observed criterion σ(I): 3 / Redundancy: 1.8 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 1.03 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 0.6 / Num. unique all: 1876

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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: 2.1→22.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.867 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24705 399 5 %RANDOM
Rwork0.19755 ---
obs0.20007 7625 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.865 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.1→22.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 0 40 1122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221107
X-RAY DIFFRACTIONr_angle_refined_deg2.2631.9791484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5265134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.34624.37548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.26215223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.116156
X-RAY DIFFRACTIONr_chiral_restr0.1770.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02809
X-RAY DIFFRACTIONr_nbd_refined0.2270.2394
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2728
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.28
X-RAY DIFFRACTIONr_mcbond_it1.81.5693
X-RAY DIFFRACTIONr_mcangle_it2.72821077
X-RAY DIFFRACTIONr_scbond_it4.0133473
X-RAY DIFFRACTIONr_scangle_it6.2314.5407
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 28 -
Rwork0.249 596 -
obs--99.52 %

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