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- PDB-3e5s: Crystal structure of Staphylococcal nuclease variant Delta+PHS L1... -

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Basic information

Entry
Database: PDB / ID: 3e5s
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS L103K at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / Calcium / Endonuclease / Membrane / Metal-binding / Nuclease / Secreted / Zymogen
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
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKhangulov, V.S. / Schlessman, J.L. / Garcia-Moreno, E.B.
CitationJournal: To be Published
Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS L103K at cryogenic temperature
Authors: Khangulov, V.S. / Schlessman, J.L. / Garcia-Moreno, E.B.
History
DepositionAug 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermonuclease
B: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2046
Polymers32,3192
Non-polymers8854
Water2,720151
1
A: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6023
Polymers16,1591
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6023
Polymers16,1591
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.172, 78.514, 60.949
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thermonuclease / TNase / Micrococcal nuclease / Staphylococcal nuclease / Nuclease B / Nuclease A


Mass: 16159.486 Da / Num. of mol.: 2 / Mutation: G50F/V51N/L103K/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-THP / THYMIDINE-3',5'-DIPHOSPHATE


Type: DNA linking / Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 46.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 35% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jul 31, 2007 / Details: multi-layer optics
RadiationMonochromator: GE111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 5.05 % / Av σ(I) over netI: 19.83 / Number: 121434 / Rsym value: 0.103 / D res high: 1.859 Å / Num. obs: 24053 / % possible obs: 97.65
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRsym value
4.0160.9510.08
3.184.0110.088
2.783.1810.105
2.522.7810.129
2.342.5210.141
2.22.3410.173
2.092.210.189
22.0910.234
1.92210.305
1.861.9210.362
ReflectionResolution: 1.859→60.95 Å / Num. all: 24646 / Num. obs: 24052 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.92 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.0658 / Rsym value: 0.0739 / Net I/σ(I): 15.7
Reflection shellResolution: 1.859→1.96 Å / Redundancy: 2.19 % / Rmerge(I) obs: 0.3219 / Mean I/σ(I) obs: 2.48 / Num. unique all: 3521 / Rsym value: 0.4179 / % possible all: 91.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.72 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å60.95 Å
Translation2.5 Å60.95 Å

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
APEXdata collection
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BDC.PDB

3bdc


Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.882 / Highest resolution: 2 Å / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.159 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.905 / SU B: 2.575 / SU ML: 0.073 / SU R Cruickshank DPI: 0.035 / SU Rfree: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.034 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 974 4.9 %RANDOM
Rwork0.164 ---
all0.167 27776 --
obs0.167 18704 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 49.01 Å2 / Biso mean: 14.49 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å20 Å2-0.01 Å2
2--5.42 Å20 Å2
3----3.36 Å2
Refine analyzeLuzzati coordinate error obs: 0.1875 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 52 151 2317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222212
X-RAY DIFFRACTIONr_angle_refined_deg1.4772.0012992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4145276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36825.10298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31415434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3731510
X-RAY DIFFRACTIONr_chiral_restr0.1260.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211618
X-RAY DIFFRACTIONr_mcbond_it2.3571.51308
X-RAY DIFFRACTIONr_mcangle_it3.10622106
X-RAY DIFFRACTIONr_scbond_it5.133904
X-RAY DIFFRACTIONr_scangle_it6.2624.5876
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2-2.0520.273930.13413381431148296.56
2.052-2.1080.283620.143142796.776
2.108-2.1690.244640.15140498.291
2.169-2.2360.19680.149134697.4
2.236-2.3090.215520.166128998.526
2.309-2.390.223610.178128898.447

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