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- PDB-3t16: Crystal structure of Staphylococcal nuclease variant NVIAGA/M98G ... -

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Basic information

Entry
Database: PDB / ID: 3t16
TitleCrystal structure of Staphylococcal nuclease variant NVIAGA/M98G at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant
Function / homology
Function and homology information


: / micrococcal nuclease / nucleic acid binding / extracellular region / metal ion binding / membrane
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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSchlessman, J.L. / Doctrow, B.M. / Garcia-Moreno E., B. / Heroux, A.
CitationJournal: To be Published
Title: Crystal structure of Staphylococcal nuclease variant NVIAGA/M98G at cryogenic temperature
Authors: Baran, K.L. / Doctrow, B.M. / Chimenti, M. / Herbst, K. / Fitch, C.A. / Majumdar, A. / Schlessman, J.L. / Garcia-Moreno E., B.
History
DepositionJul 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermonuclease


Theoretical massNumber of molelcules
Total (without water)16,7061
Polymers16,7061
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.649, 48.649, 63.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 16706.219 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: D21N/T33V/T41I/S59A/M98G/P117G/S128A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 41% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 13663 / Num. obs: 13663 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.043 / Χ2: 1.681 / Net I/σ(I): 22
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.8314.80.2956681.0341100
1.83-1.8614.90.2377101.0261100
1.86-1.9150.2326751.0771100
1.9-1.9414.90.1696881.1771100
1.94-1.98150.136491.2681100
1.98-2.03150.1227181.3381100
2.03-2.08150.0996681.41100
2.08-2.1314.90.0816881.5311100
2.13-2.2150.0756681.6011100
2.2-2.2714.90.0656861.5521100
2.27-2.35150.066901.5921100
2.35-2.4414.90.0556921.6771100
2.44-2.5514.90.056721.6951100
2.55-2.69150.0456891.8061100
2.69-2.8614.90.0446941.8451100
2.86-3.0814.80.0456842.3991100
3.08-3.3914.60.0446782.883199.9
3.39-3.8814.20.0436962.9951100
3.88-4.8813.50.0327022.046199.7
4.88-5013.50.0316481.804191.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.33 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.53 Å
Translation2.5 Å26.53 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 2RDF

2rdf


Resolution: 1.8→48.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.2256 / WRfactor Rwork: 0.1997 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8226 / SU B: 6.933 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1171 / SU Rfree: 0.1114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 678 5 %RANDOM
Rwork0.1811 ---
all0.1825 13637 --
obs0.1825 13637 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 92.83 Å2 / Biso mean: 44.2723 Å2 / Biso min: 26.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 0 71 1056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221025
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.9721379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45224.44445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.90615200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.942155
X-RAY DIFFRACTIONr_chiral_restr0.1380.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021754
X-RAY DIFFRACTIONr_mcbond_it1.1671.5621
X-RAY DIFFRACTIONr_mcangle_it1.9532993
X-RAY DIFFRACTIONr_scbond_it3.6833404
X-RAY DIFFRACTIONr_scangle_it5.9434.5383
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 53 -
Rwork0.243 958 -
all-1011 -
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)
19.41585.94544.08123.487-1.340314.15980.2119-0.2560.7515-0.17360.44721.47370.3032-2.0763-0.65910.47960.0255-0.06480.61010.13590.4368-12.4316.265-4.76
25.48512.21810.67562.87671.33747.45150.30910.1842-0.4296-0.11690.1562-0.00591.2620.0304-0.46530.630.0718-0.10180.30010.0180.2073-0.8998.536-3.904
30.98550.62782.80133.4833.076915.3379-0.08480.29850.21590.03720.4888-0.6194-0.4082.0202-0.4040.49130.00060.01360.6199-0.08850.30948.24221.3040.036
48.21023.9888-0.56265.74810.20510.62050.2769-0.4921-0.33160.44060.1575-0.40351.05690.505-0.43440.55210.123-0.06270.41620.02320.21143.88413.4238.423
51.67371.2962.0024.1367-2.20068.80870.0623-0.043-0.0062-0.0890.09760.1670.0619-0.5718-0.15990.46870.0305-0.01580.35210.03680.1904-5.49717.08-6.753
61.78661.70141.09742.67510.359.66270.01180.0455-0.0488-0.02030.06020.02440.099-0.0571-0.0720.44740.04980.00210.32810.04390.1675-1.94416.717-4.287
71.85490.4132.14592.13862.26599.371-0.07880.12210.0489-0.37290.2040.05-1.03240.4248-0.12520.54190.00590.03460.3444-0.00590.16741.31525.684-1.111
87.29350.07186.06122.57222.659617.6226-0.17760.07340.4042-0.79490.0945-0.1476-2.53510.29090.08320.9294-0.01850.06710.2754-0.00970.1521.48233.2643.68
910.4562-0.1674-0.075612.153-2.170717.08880.05250.04170.1429-0.56410.614-0.9599-1.16492.0523-0.66650.536-0.24010.09780.7296-0.19090.23610.4330.11610.719
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 12
2X-RAY DIFFRACTION2A13 - 34
3X-RAY DIFFRACTION3A35 - 55
4X-RAY DIFFRACTION4A56 - 68
5X-RAY DIFFRACTION5A69 - 84
6X-RAY DIFFRACTION6A85 - 96
7X-RAY DIFFRACTION7A97 - 121
8X-RAY DIFFRACTION8A122 - 134
9X-RAY DIFFRACTION9A135 - 141

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