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- PDB-6xse: Crystal structure of Staphylococcal nuclease variant Delta+PHS F3... -

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Basic information

Entry
Database: PDB / ID: 6xse
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS F34Y at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / nuclease / polar group / pdTp
Function / homology
Function and homology information


micrococcal nuclease / : / nucleic acid binding / extracellular region / metal ion binding / membrane
Similarity search - Function
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
Similarity search - Domain/homology
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsRobinson, A.C. / 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) United States
CitationJournal: To be Published
Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS F34Y at cryogenic temperature
Authors: Robinson, A.C. / Schlessman, J.L. / Garcia-Moreno E., B.
History
DepositionJul 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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)16,6023
Polymers16,1591
Non-polymers4422
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-15 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.958, 61.309, 38.051
Angle α, β, γ (deg.)90.000, 92.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16159.463 Da / Num. of mol.: 1 / Fragment: UNP residues 83-231 / Mutation: F34Y/G50F/V51N/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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 44.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 26% MPD, 25 mM potassium phosphate, calcium chloride, THP

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→38 Å / Num. obs: 8368 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.021 / Net I/σ(I): 41.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 5.77 / Num. unique obs: 844 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.39 Å24.62 Å
Translation4.39 Å24.62 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BDC

3bdc


Resolution: 2.1→24.63 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2342 / WRfactor Rwork: 0.1986 / FOM work R set: 0.7041 / SU B: 9.209 / SU ML: 0.229 / SU R Cruickshank DPI: 0.2706 / SU Rfree: 0.2205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2791 417 5 %RANDOM
Rwork0.2306 ---
obs0.2331 7937 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.4 Å2 / Biso mean: 32.973 Å2 / Biso min: 17.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.02 Å2
2--0.05 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.1→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 0 26 25 1085
Biso mean--31.45 32.79 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131078
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171035
X-RAY DIFFRACTIONr_angle_refined_deg1.541.6941451
X-RAY DIFFRACTIONr_angle_other_deg1.3381.6092410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63223.46252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47115208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.37155
X-RAY DIFFRACTIONr_chiral_restr0.0550.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02208
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 23 -
Rwork0.322 572 -
all-595 -
obs--100 %

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