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- PDB-9cii: Crystal structure of Staphylococcal nuclease variant Delta+PHS V2... -

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Basic information

Entry
Database: PDB / ID: 9cii
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS V23D/L36R at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / ARGININE / ION-PAIR / STAPHYLOCOCCAL NUCLEASE
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: 1.85 Å
AuthorsZhang, Y. / Schlessman, J.L. / Robinson, A.C. / 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 V23D/L36R 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)16,6463
Polymers16,2031
Non-polymers4422
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.172, 60.277, 38.350
Angle α, β, γ (deg.)90.00, 93.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16203.459 Da / Num. of mol.: 1 / Mutation: V23D, L36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc, SACOL0860 / Plasmid: pET24a+ / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 30% MPD, 25mM Potassium Phosphate

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.5418 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Aug 4, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→23.66 Å / Num. obs: 12187 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 16.26 Å2 / Rmerge(I) obs: 0.024 / Rsym value: 0.083 / Net I/σ(I): 36.95
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 4.91 / Num. unique obs: 1225 / Rsym value: 0.256 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisPro41.93a 64-bit (release 15-12-2020)data scaling
CrysalisPro41.93a 64-bit (release 15-12-2020)data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→23.42 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.651 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20887 622 5.1 %RANDOM
Rwork0.16615 ---
obs0.16836 11549 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 mean: 24.279 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å20.29 Å2
2---0.81 Å20 Å2
3---1.26 Å2
Refinement stepCycle: 1 / Resolution: 1.85→23.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 26 151 1214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121110
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161092
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.8761502
X-RAY DIFFRACTIONr_angle_other_deg0.5661.8062525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8095138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.82356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63110217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021265
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
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_it1.9422.076525
X-RAY DIFFRACTIONr_mcbond_other1.9222.075525
X-RAY DIFFRACTIONr_mcangle_it2.8943.728657
X-RAY DIFFRACTIONr_mcangle_other2.8983.731658
X-RAY DIFFRACTIONr_scbond_it3.0812.485585
X-RAY DIFFRACTIONr_scbond_other3.0782.484586
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8794.34841
X-RAY DIFFRACTIONr_long_range_B_refined6.38526.324832
X-RAY DIFFRACTIONr_long_range_B_other6.23925.824688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 52 -
Rwork0.191 829 -
obs--100 %

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