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- PDB-6ok8: Crystal structure of Staphylococcal nuclease variant Delta+PHS K1... -

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Basic information

Entry
Database: PDB / ID: 6ok8
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS K127L at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / nuclease / hyperstable / pdTp / ionizable group
Function / homology
Function and homology information


micrococcal nuclease / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / nucleic acid binding / extracellular region / membrane / 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
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsJeliazkov, J.R. / Robinson, A.C. / Berger, J.M. / Garcia-Moreno E., B. / Gray, J.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Toward the computational design of protein crystals with improved resolution.
Authors: Jeliazkov, J.R. / Robinson, A.C. / Garcia-Moreno E, B. / Berger, J.M. / Gray, J.J.
History
DepositionApr 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.4Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5703
Polymers16,1271
Non-polymers4422
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-9 kcal/mol
Surface area7080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.097, 48.097, 63.122
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: 16127.441 Da / Num. of mol.: 1 / Fragment: UNP residues 83-231 / Mutation: G50F/V51N/P117G/H124L/K127L/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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-THP / THYMIDINE-3',5'-DIPHOSPHATE


Type: DNA linking / Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 46% MPD, 25 mM potassium phosphate, calcium chloride, THP

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→48.1 Å / Num. obs: 12313 / % possible obs: 91.8 % / Redundancy: 5.877 % / Biso Wilson estimate: 29.93 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.032 / Χ2: 1.041 / Net I/σ(I): 35.75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.851.850.1015.344870.9780.13448.7
1.85-1.92.5010.1067.076570.9870.13269.5
1.9-1.953.5420.09511.447800.9910.11183.2
1.95-2.015.5140.07617.188780.9960.08496.1
2.01-2.086.0530.06322.458640.9980.06997.6
2.08-2.156.2910.05128.338270.9980.05698.1
2.15-2.236.4250.04929.957910.9980.05397.9
2.23-2.326.3950.04933.597950.9990.05498.3
2.32-2.436.730.04137.297550.9990.04498.6
2.43-2.546.9360.03840.587180.9990.04198.9
2.54-2.686.9220.03544.356830.9990.03799.4
2.68-2.846.8780.03445.36620.9990.03699.5
2.84-3.046.9090.03249.686060.9990.03499.3
3.04-3.286.7340.02853.695710.9990.0399.7
3.28-3.66.5710.02759.225340.9990.029100
3.6-4.026.4560.02560.694890.9990.02799.8
4.02-4.656.5380.02464.134160.9990.026100
4.65-5.696.2790.02362.0936210.025100
5.69-8.055.9820.02361.692830.9990.026100
8.05-48.15.7680.01960.7615510.0297.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.36 Å38.26 Å
Translation4.36 Å38.26 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
XSCALEdata scaling
PHASER2.8.1phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BDC

3bdc


Resolution: 1.8→48.1 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.1504 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.133 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 619 5 %RANDOM
Rwork0.1988 ---
obs0.2001 11694 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.97 Å2 / Biso mean: 25.922 Å2 / Biso min: 11.83 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.8→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 26 89 1147
Biso mean--34.2 31.22 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191075
X-RAY DIFFRACTIONr_angle_refined_deg1.8662.0071446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9085127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.37824.89447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56215206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.174155
X-RAY DIFFRACTIONr_chiral_restr0.1320.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021777
LS refinement shellResolution: 1.799→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 24 -
Rwork0.264 462 -
all-486 -
obs--48.55 %

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