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- PDB-5i6w: Crystal structure of Staphylococcal nuclease variant Delta+PHS A5... -

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Basic information

Entry
Database: PDB / ID: 5i6w
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS A58D at cryogenic temperature
ComponentsThermonucleaseMicrococcal nuclease
KeywordsHYDROLASE / nuclease / hyperstable / pdTp / 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
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSkerritt, L.A. / 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 A58D at cryogenic temperature
Authors: Skerritt, L.A. / Schlessman, J.L. / Garcia-Moreno E., B.
History
DepositionFeb 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 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 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)16,6303
Polymers16,1871
Non-polymers4422
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-14 kcal/mol
Surface area6960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.178, 60.353, 38.425
Angle α, β, γ (deg.)90.000, 93.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16187.475 Da / Num. of mol.: 1 / Fragment: UNP residues 80-228 / Mutation: G50F/V51N/A58D/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-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 / Thymidine diphosphate


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


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% 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: 1.5418 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jan 19, 2016
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 11235 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 26.93 Å2 / Rmerge(I) obs: 0.018 / Net I/σ(I): 54.17
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 7.17 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.89 Å27.66 Å
Translation1.89 Å27.66 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
CrysalisPro1.171.36.32data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.2data extraction
CrysalisPro1.171.36.32data reduction
Coot0.7.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BDC

3bdc


Resolution: 1.9→38.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.595 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1588 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 598 5.3 %RANDOM
Rwork0.1814 ---
obs0.1842 10622 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.41 Å2 / Biso mean: 26.866 Å2 / Biso min: 12.34 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å20.57 Å2
2---2.53 Å2-0 Å2
3---4.71 Å2
Refinement stepCycle: final / Resolution: 1.9→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 26 76 1138
Biso mean--20.37 26.31 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191146
X-RAY DIFFRACTIONr_bond_other_d0.0010.021141
X-RAY DIFFRACTIONr_angle_refined_deg1.7922.0011557
X-RAY DIFFRACTIONr_angle_other_deg0.86832652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2765147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52825.19252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30515231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.41155
X-RAY DIFFRACTIONr_chiral_restr0.1160.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021271
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02248
X-RAY DIFFRACTIONr_mcbond_it1.3181.508535
X-RAY DIFFRACTIONr_mcbond_other1.31.506534
X-RAY DIFFRACTIONr_mcangle_it2.0792.254672
LS refinement shellResolution: 1.9→1.94 Å
RfactorNum. reflection% reflection
Rfree0.274 28 -
Rwork0.252 612 -
obs--76.28 %
Refinement TLS params.Method: refined / Origin x: 37.6651 Å / Origin y: 4.2147 Å / Origin z: 43.4702 Å
111213212223313233
T0.0619 Å2-0.0033 Å2-0.0004 Å2-0.0879 Å20.0152 Å2--0.0049 Å2
L2.2232 °2-0.3827 °2-0.1732 °2-2.6273 °20.3234 °2--0.9627 °2
S-0.0404 Å °-0.1436 Å °0.0165 Å °0.128 Å °0.0356 Å °0.0574 Å °-0.0125 Å °0.0109 Å °0.0048 Å °

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