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- PDB-6eek: Crystal structure of apo Staphylcoccal nuclease variant Delta+PHS... -

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Basic information

Entry
Database: PDB / ID: 6eek
TitleCrystal structure of apo Staphylcoccal nuclease variant Delta+PHS T62E/V66K, pH 7 at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / nuclease / hyperstable / ionizable group
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 / molecular replacement / Resolution: 2.2 Å
AuthorsKougentakis, C.M. / Schlessman, J.L. / Garcia-Moreno, E.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM061597 United States
CitationJournal: To be Published
Title: Crystal structure of apo Staphylcoccal nuclease variant Delta+PHS T62E/V66K, pH 7 at cryogenic temperature
Authors: Kougentakis, C.M. / Schlessman, J.L. / Garcia-Moreno, E.B.
History
DepositionAug 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,2021
Polymers16,2021
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.795, 71.795, 56.804
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Thermonuclease / TNase / Micrococcal nuclease / Staphylococcal nuclease


Mass: 16201.523 Da / Num. of mol.: 1 / Fragment: UNP residues 83-231 / Mutation: G50F/V51N/T62E/V66K/P117G/H124L/S128A/Del44-49
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: pET24a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00644, micrococcal nuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM HEPES, 29% Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Oct 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→62.18 Å / Num. obs: 8555 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 42.05 Å2 / Rmerge(I) obs: 0.023 / Net I/σ(I): 44.56
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 6.05 / Num. unique obs: 860 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.93 Å18.11 Å
Translation4.93 Å18.11 Å

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Processing

Software
NameVersionClassification
PHASER2.5.7phasing
REFMAC5.8.0124refinement
PDB_EXTRACT3.24data extraction
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BDC

3bdc


Resolution: 2.2→62.18 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.874 / SU B: 21.407 / SU ML: 0.235 / SU R Cruickshank DPI: 0.271 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.238 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3086 399 4.7 %RANDOM
Rwork0.2538 ---
obs0.2564 8146 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.64 Å2 / Biso mean: 42.055 Å2 / Biso min: 21.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.19 Å20 Å2
2--0.39 Å20 Å2
3----1.25 Å2
Refinement stepCycle: final / Resolution: 2.2→62.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms964 0 0 7 971
Biso mean---28.5 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.019981
X-RAY DIFFRACTIONr_bond_other_d0.0030.02975
X-RAY DIFFRACTIONr_angle_refined_deg2.2591.9781311
X-RAY DIFFRACTIONr_angle_other_deg1.17532251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45824.78346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.01915196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.137155
X-RAY DIFFRACTIONr_chiral_restr0.150.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021084
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02217
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.507 26 -
Rwork0.338 596 -
all-622 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 9.6495 Å / Origin y: 69.1648 Å / Origin z: 3.9064 Å
111213212223313233
T0.0617 Å20.0187 Å2-0.0103 Å2-0.0242 Å2-0.0096 Å2--0.3957 Å2
L4.9485 °21.2861 °20.2071 °2-2.1648 °20.3908 °2--2.1654 °2
S-0.0122 Å °0.1526 Å °-0.5019 Å °0.1128 Å °-0.0025 Å °-0.2238 Å °0.2133 Å °0.1263 Å °0.0147 Å °

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