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- PDB-3sk8: Crystal structure of Staphylococcal nuclease variant Delta+PHS M9... -

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Basic information

Entry
Database: PDB / ID: 3sk8
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS M98G apo protein at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant
Function / homology
Function and homology information


micrococcal nuclease / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / nucleic acid binding / extracellular region / membrane / metal ion binding
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsDoctrow, B.M. / Schlessman, J.L. / Garcia-Moreno E., B. / Heroux, A.
CitationJournal: To be Published
Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS M98G apo protein at cryogenic temperature
Authors: Doctrow, B.M. / Schlessman, J.L. / Garcia-Moreno E., B.
History
DepositionJun 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)16,3774
Polymers16,0691
Non-polymers3083
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.372, 48.372, 63.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 16069.318 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: G50F/V51N/M98G/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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00644, micrococcal nuclease
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 34% MPD, 25 mM potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2010
Details: Meridianally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 11646 / Num. obs: 11646 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.073 / Χ2: 2.275 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.9313.10.2835811.044199.3
1.93-1.9713.50.2655611.2161100
1.97-2.01140.2376011.285199.5
2.01-2.05140.2135701.3741100
2.05-2.0914.20.1935911.566199.7
2.09-2.14140.175751.73199.7
2.14-2.1913.80.1615771.938199.8
2.19-2.2513.70.1485552.0471100
2.25-2.3213.80.145992.122199.8
2.32-2.3913.90.1255642.212199.8
2.39-2.4813.70.1175852.3051100
2.48-2.5813.60.1085972.521100
2.58-2.713.50.0965802.6061100
2.7-2.8413.40.0865912.7161100
2.84-3.0213.10.0815802.9091100
3.02-3.2512.70.0695813.11100
3.25-3.5812.40.0625803.4521100
3.58-4.0912.30.0585903.4491100
4.09-5.1612.80.0525943.198199.5
5.16-5013.50.0555943.089196.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.62 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.47 Å
Translation2.5 Å38.47 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BDC

3bdc


Resolution: 1.9→48.37 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2153 / WRfactor Rwork: 0.1717 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8671 / SU B: 6.522 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1369 / SU Rfree: 0.1322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21 555 4.8 %RANDOM
Rwork0.1648 ---
all0.1669 11629 --
obs0.1669 11629 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 37.75 Å2 / Biso mean: 12.6141 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.59 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 18 96 1143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221105
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9951495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1035142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0625.10249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92115220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.22155
X-RAY DIFFRACTIONr_chiral_restr0.1590.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021807
X-RAY DIFFRACTIONr_mcbond_it1.3821.5659
X-RAY DIFFRACTIONr_mcangle_it2.0621061
X-RAY DIFFRACTIONr_scbond_it3.6063446
X-RAY DIFFRACTIONr_scangle_it5.4454.5427
LS refinement shellResolution: 1.896→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 52 -
Rwork0.181 805 -
all-857 -
obs--99.19 %
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)
13.4266-0.71540.39952.0928-0.03972.994-0.08970.07450.12960.03840.15040.0139-0.3382-0.0011-0.06080.2216-0.01510.00220.166-0.00140.119-3.124-11.1112.908
21.8974-0.19280.60812.27020.82664.3656-0.1939-0.13640.10270.19090.3555-0.0262-0.30790.2769-0.16150.2099-0.06020.00770.2048-0.01550.13511.354-13.8195.706
33.7994-0.8002-0.40572.39731.20394.00190.08650.31540.1341-0.3450.277-0.3995-0.45550.6997-0.36350.1972-0.15080.05290.2953-0.0560.16087.281-14.787-6.715
40.6870.45151.60562.21710.53364.2056-0.1026-0.18850.0257-0.21160.0230.0975-0.1432-0.24720.07950.2454-0.01450.00530.26050.01730.116-8.208-17.3165.153
51.7075-0.41650.21161.15531.83283.9918-0.0596-0.20210.1160.06230.17490.02860.06160.0556-0.11530.2005-0.0417-0.01040.18520.0080.1243-1.184-16.6888.45
61.40740.2322-0.00270.87880.34478.1442-0.01220.24240.0212-0.12950.30930.00990.0750.3059-0.2970.1978-0.0325-0.0030.13590.01280.08090.927-23.437-5.706
71.6124-0.3857-1.53521.30651.8028.50490.0395-0.0284-0.10920.08480.1467-0.10131.07030.4437-0.18610.24910.0827-0.05410.1089-0.00830.05763.541-30.081-0.364
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 26
2X-RAY DIFFRACTION2A27 - 50
3X-RAY DIFFRACTION3A51 - 69
4X-RAY DIFFRACTION4A70 - 80
5X-RAY DIFFRACTION5A81 - 96
6X-RAY DIFFRACTION6A97 - 109
7X-RAY DIFFRACTION7A110 - 141

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