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- PDB-5k5p: Crystal structure of Staphylococcal nuclease variant Delta+PHS I7... -

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Basic information

Entry
Database: PDB / ID: 5k5p
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS I72K L103K at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / nuclease / hyperstable / pdTp / ionizable group / pH switch
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
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsSorenson, J.L. / 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 Staphylococcal nuclease variant Delta+PHS I72K L103K at cryogenic temperature
Authors: Sorenson, J.L. / Schlessman, J.L. / Garcia-Moreno E., B.
History
DepositionMay 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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)16,5782
Polymers16,1761
Non-polymers4021
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-3 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.120, 61.640, 80.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 16175.510 Da / Num. of mol.: 1 / Fragment: UNP residues 83-231 / Mutation: G50F/V51N/I72K/L103K/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: Chemical ChemComp-THP / THYMIDINE-3',5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 13844 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 60.29
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 13.35 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XPREPdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BDC

3bdc


Resolution: 1.83→48.92 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.899 / SU B: 2.978 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23744 720 5.2 %RANDOM
Rwork0.18849 ---
obs0.19096 13080 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.335 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.83→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 25 98 1158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021138
X-RAY DIFFRACTIONr_bond_other_d0.0060.021148
X-RAY DIFFRACTIONr_angle_refined_deg1.8132.0061544
X-RAY DIFFRACTIONr_angle_other_deg0.89732664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1472548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84815230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.208155
X-RAY DIFFRACTIONr_chiral_restr0.1120.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021258
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02243
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9410.888539
X-RAY DIFFRACTIONr_mcbond_other0.9230.887538
X-RAY DIFFRACTIONr_mcangle_it1.4031.327679
X-RAY DIFFRACTIONr_mcangle_other1.4051.328680
X-RAY DIFFRACTIONr_scbond_it1.951.206599
X-RAY DIFFRACTIONr_scbond_other1.9481.204595
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1271.688853
X-RAY DIFFRACTIONr_long_range_B_refined4.4177.8041354
X-RAY DIFFRACTIONr_long_range_B_other4.4167.8121355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 73 -
Rwork0.222 932 -
obs--100 %

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