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- PDB-9cil: Crystal structure of Staphylococcal nuclease variant Delta+PHS T4... -

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Basic information

Entry
Database: PDB / ID: 9cil
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS T41V/S59A at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / STAPHYLOCOCCAL NUCLEASE / HYPERSTABLE VARIANT / REFERENCE
Function / homology
Function and homology information


micrococcal nuclease / : / nucleic acid binding / extracellular region / metal ion binding
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 / Resolution: 2 Å
AuthorsZhang, Y. / Schlessman, J.L. / Siegler, M.A. / Garcia-Moreno E., B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 061597 United States
CitationJournal: To Be Published
Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS T41V/S59A at cryogenic temperature
Authors: Zhang, Y. / Schlessman, J.L. / Robinson, A.C. / Garcia-Moreno E., B.
History
DepositionJul 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5683
Polymers16,1251
Non-polymers4422
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.021, 60.753, 38.429
Angle α, β, γ (deg.)90.00, 92.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16125.490 Da / Num. of mol.: 1 / Mutation: T41V, S59A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc, SACOL0860 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5HHM4, 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.: 73 / 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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 35% MPD, 25 mM Potassium Phosphate,

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jun 28, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→21.92 Å / Num. obs: 9707 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 20.71 Å2 / Rmerge(I) obs: 0.013 / Rsym value: 0.086 / Net I/σ(I): 76.43
Reflection shellResolution: 2→2.07 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 11.37 / Num. unique obs: 799 / Rsym value: 0.208 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisPro42.80a 64-bit (release 13-01-2023)data scaling
CrysalisPro42.80a 64-bit (release 13-01-2023)data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→21.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.585 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 461 4.8 %RANDOM
Rwork0.18491 ---
obs0.1872 9232 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.448 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å20.43 Å2
2---0.28 Å20 Å2
3---1.71 Å2
Refinement stepCycle: 1 / Resolution: 2→21.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 26 73 1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121076
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161059
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.8751448
X-RAY DIFFRACTIONr_angle_other_deg0.5931.82446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.59755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45110207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02231
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_it3.212.732515
X-RAY DIFFRACTIONr_mcbond_other3.2112.73515
X-RAY DIFFRACTIONr_mcangle_it4.3534.886642
X-RAY DIFFRACTIONr_mcangle_other4.3724.89643
X-RAY DIFFRACTIONr_scbond_it4.3313.298561
X-RAY DIFFRACTIONr_scbond_other4.3273.295562
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4635.76807
X-RAY DIFFRACTIONr_long_range_B_refined8.52133.934523
X-RAY DIFFRACTIONr_long_range_B_other8.51833.84482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 31 -
Rwork0.206 670 -
obs--100 %

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