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- PDB-2pyk: Crystal structure of Staphylococcal nuclease variant V66Q/P117G/H... -

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Basic information

Entry
Database: PDB / ID: 2pyk
TitleCrystal structure of Staphylococcal nuclease variant V66Q/P117G/H124L/S128A at room temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / nuclease / hyperstable variant / internal waters
Function / homology
Function and homology information


micrococcal nuclease / : / nucleic acid binding / extracellular region / metal ion binding
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
Thermonuclease / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchlessman, J.L. / Abe, C. / Garcia-Moreno, E.B.
CitationJournal: Biophys.J. / Year: 2008
Title: Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups.
Authors: Schlessman, J.L. / Abe, C. / Gittis, A. / Karp, D.A. / Dolan, M.A. / Garcia-Moreno, E.B.
History
DepositionMay 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermonuclease


Theoretical massNumber of molelcules
Total (without water)16,7911
Polymers16,7911
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.967, 48.967, 63.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 16791.275 Da / Num. of mol.: 1 / Mutation: V66Q, P117G, H124L, S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: lambda / Production host: Escherichia coli (E. coli) / Strain (production host): AR120
References: UniProt: Q8NXI6, UniProt: A5A513*PLUS, micrococcal nuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 37% MPD, 0.025 M potassium phosphate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418
DetectorType: APEX II CCD / Detector: CCD / Date: Mar 15, 2006
RadiationMonochromator: GE111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 8881 / Num. obs: 8861 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.0229 / Net I/σ(I): 32.85
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.89 % / Rmerge(I) obs: 0.1344 / Mean I/σ(I) obs: 7.09 / Num. unique all: 1141 / % possible all: 100

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.716 / Packing: 0.52
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation3 Å15 Ågeneral100 0

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
APEXdata collection
APEXdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Staphyloccocal nuclease V66E/P117G/H124L/S128A variant (at 100K), with b-factors set to 20.0 A^2 and residue 66 truncated to Ala, waters excluded

100k


Resolution: 2.1→50 Å / FOM work R set: 0.844 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 938 10.6 %random
Rwork0.186 ---
all0.203 8810 --
obs0.203 8810 99.4 %-
Solvent computationBsol: 64.307 Å2
Displacement parametersBiso mean: 30.354 Å2
Baniso -1Baniso -2Baniso -3
1--2.945 Å20 Å20 Å2
2---2.945 Å20 Å2
3---5.89 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 0 0 38 1077
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4131.5
X-RAY DIFFRACTIONc_scbond_it2.5732
X-RAY DIFFRACTIONc_mcangle_it2.1422
X-RAY DIFFRACTIONc_scangle_it3.8952.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.1-2.140.32560.216430486
2.14-2.180.27440.215427471
2.18-2.230.314500.203444494
2.23-2.280.259460.211421467
2.28-2.340.271480.203452500
2.34-2.40.214490.172418467
2.4-2.470.225600.191435495
2.47-2.550.254450.213433478
2.55-2.650.246470.213444491
2.65-2.750.313600.219445505
2.75-2.880.246550.205437492
2.88-3.030.315600.216426486
3.03-3.220.183440.178442486
3.22-3.470.203530.164445498
3.47-3.820.189600.152432492
3.82-4.370.199470.142440487
4.37-5.50.2520.163453505
5.5-500.227620.223448510
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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