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

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Basic information

Entry
Database: PDB / ID: 9cik
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS V23R/L36D at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / STAPHYLOCOCCAL NUCLEASE / ARGININE / ION PAIR
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: 1.95 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 V23R/L36D 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
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.875, 60.382, 38.196
Angle α, β, γ (deg.)90.00, 94.06, 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: V23R, L36D
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.: 103 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 28% MPD, 25 mM 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: Dec 15, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20.11 Å / Num. obs: 10282 / % possible obs: 99.9 % / Redundancy: 16 % / Rmerge(I) obs: 0.016 / Rsym value: 0.049 / Net I/σ(I): 53.8
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 5.85 / Num. unique obs: 1030 / Rsym value: 0.305 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisPro42.49 64-bit (release 15-03-2022)data scaling
CrysalisPro42.49 64-bit (release 15-03-2022)data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.18 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.975 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20829 489 4.8 %RANDOM
Rwork0.17133 ---
obs0.17308 9777 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.257 Å2
Baniso -1Baniso -2Baniso -3
1--2.48 Å2-0 Å20.08 Å2
2---0.54 Å20 Å2
3---2.98 Å2
Refinement stepCycle: 1 / Resolution: 1.95→19.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 26 103 1166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121103
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161081
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.8771491
X-RAY DIFFRACTIONr_angle_other_deg0.591.8082498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1095136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.49656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27710214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02242
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_it0.9630.902523
X-RAY DIFFRACTIONr_mcbond_other0.9540.901523
X-RAY DIFFRACTIONr_mcangle_it1.4811.612654
X-RAY DIFFRACTIONr_mcangle_other1.4841.614655
X-RAY DIFFRACTIONr_scbond_it2.1851.215580
X-RAY DIFFRACTIONr_scbond_other2.1831.216581
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2512.116834
X-RAY DIFFRACTIONr_long_range_B_refined5.96212.564782
X-RAY DIFFRACTIONr_long_range_B_other5.84411.794696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 34 -
Rwork0.227 708 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.5244-4.23621.29669.0521-3.43467.6660.07490.4136-1.3352-0.079-0.09170.41120.7426-0.18290.01680.197-0.01950.06120.0415-0.07890.2210.242-5.9931.468
25.2705-1.699-0.92484.04545.07156.6863-0.2440.0015-0.56230.43950.18640.1660.50710.28860.05760.30010.04170.04420.2109-0.00240.143515.741-1.6975.556
33.8344-4.94070.07166.647-0.13040.0077-0.07220.1757-0.2470.00520.04960.10140.026-0.03440.02250.328-0.02230.090.3302-0.15070.293116.794-2.5830.349
47.9574-2.3680.2842.66641.23951.2322-0.2642-0.4787-0.05250.24240.19940.27150.1040.0340.06480.2603-0.0020.05230.18980.01720.070810.0373.4489.102
58.9705-0.1618-0.54953.8822-0.72281.57070.05120.7364-0.2712-0.1178-0.12770.11380.09430.03360.07650.21680.00920.03880.2233-0.03430.061711.9642.326-0.1
68.2264-2.4932-0.62783.85081.31091.83680.01170.33660.6308-0.05970.01710.55060.0352-0.1277-0.02890.1746-0.01790.01950.15860.07830.2812.9411.0793.669
727.30212.34049.14569.307-0.35358.4654-0.1749-0.93082.31430.4728-0.44191.1588-0.6866-0.30.61690.27970.12910.11350.3703-0.21350.44980.47816.80815.873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 17
2X-RAY DIFFRACTION2A18 - 27
3X-RAY DIFFRACTION3A28 - 36
4X-RAY DIFFRACTION4A37 - 74
5X-RAY DIFFRACTION5A75 - 91
6X-RAY DIFFRACTION6A92 - 126
7X-RAY DIFFRACTION7A127 - 135

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