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

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Basic information

Entry
Database: PDB / ID: 9cij
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS V23E/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: 1.9 Å
AuthorsZhang, Y. / Schlessman, L.J. / 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 V23E/L36R at cryogenic temperature
Authors: Zhang, Y. / Schlessman, L.J. / 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)16,6603
Polymers16,2171
Non-polymers4422
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.031, 60.384, 38.303
Angle α, β, γ (deg.)90.00, 93.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16217.484 Da / Num. of mol.: 1 / Mutation: V23E, L36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / 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 / 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.: 114 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 35% 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: Nov 20, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→24.9 Å / Num. obs: 11216 / % possible obs: 99.9 % / Redundancy: 10 % / Rmerge(I) obs: 0.022 / Rsym value: 0.05 / Net I/σ(I): 40
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 5.04 / Num. unique obs: 1127 / Rsym value: 0.255 / % 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: 1.9→24.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.668 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20105 538 4.8 %RANDOM
Rwork0.16535 ---
obs0.16706 10663 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.499 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å2-0.04 Å2
2---0.77 Å2-0 Å2
3---1.52 Å2
Refinement stepCycle: 1 / Resolution: 1.9→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 26 114 1178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121095
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161071
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.8811474
X-RAY DIFFRACTIONr_angle_other_deg0.561.8082476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2355132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.59956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69510215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02240
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_it1.4251.373519
X-RAY DIFFRACTIONr_mcbond_other1.4251.373519
X-RAY DIFFRACTIONr_mcangle_it2.1282.459648
X-RAY DIFFRACTIONr_mcangle_other2.1282.461649
X-RAY DIFFRACTIONr_scbond_it2.5331.758576
X-RAY DIFFRACTIONr_scbond_other2.531.757577
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.053.036825
X-RAY DIFFRACTIONr_long_range_B_refined5.98218.034686
X-RAY DIFFRACTIONr_long_range_B_other5.86917.474596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 32 -
Rwork0.194 805 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 8.667 Å / Origin y: 4.82 Å / Origin z: 5.422 Å
111213212223313233
T0.0233 Å2-0.0033 Å20.0093 Å2-0.057 Å20.0182 Å2--0.0147 Å2
L3.2301 °2-0.5506 °2-0.341 °2-3.5624 °20.3177 °2--1.2002 °2
S-0.0481 Å °-0.1178 Å °-0.0258 Å °0.0899 Å °0.0551 Å °0.147 Å °0.0726 Å °-0.0137 Å °-0.0071 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 141
2X-RAY DIFFRACTION1A201

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