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- PDB-6xsc: Crystal structure of Staphylococcal nuclease variant Delta+PHS V2... -

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Basic information

Entry
Database: PDB / ID: 6xsc
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS V23T at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / nuclease / hyperstable / OB-fold / internal polar group / pdTp
Function / homology
Function and homology information


: / micrococcal nuclease / nucleic acid binding / extracellular region / metal ion binding / membrane
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: 2 Å
AuthorsRobinson, A.C. / Schlessman, J.L. / 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 V23T at cryogenic temperature
Authors: Robinson, A.C. / Schlessman, J.L. / Garcia-Moreno E., B.
History
DepositionJul 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Author supporting evidence / Data collection / Refinement description
Category: pdbx_audit_support / reflns_shell / software
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number ..._pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _reflns_shell.d_res_high / _reflns_shell.d_res_low
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,5883
Polymers16,1451
Non-polymers4422
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-15 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.030, 60.530, 38.097
Angle α, β, γ (deg.)90.000, 93.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16145.436 Da / Num. of mol.: 1 / Fragment: UNP residues 83-231 / Mutation: V23T/G50F/V51N/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 BL21(DE3) (bacteria) / References: UniProt: P00644, 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.: 43 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% MPD, 25 mM potassium phosphate, calcium chloride

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→38.04 Å / Num. obs: 9461 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 37.26
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.79 / Num. unique obs: 961 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMACrefinement
APEX 2data reduction
CrysalisProdata scaling
PHASERphasing
REFMAC5.8.0218model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BDC

3bdc


Resolution: 2→38.04 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.433 / SU ML: 0.165 / SU R Cruickshank DPI: 0.2077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.183
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 453 4.7 %RANDOM
Rwork0.2114 ---
obs0.2136 9125 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.59 Å2 / Biso mean: 32.725 Å2 / Biso min: 17.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.02 Å2
2--0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1033 0 26 43 1102
Biso mean--30.99 30.76 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191077
X-RAY DIFFRACTIONr_bond_other_d0.0060.021033
X-RAY DIFFRACTIONr_angle_refined_deg1.6862.0051449
X-RAY DIFFRACTIONr_angle_other_deg0.77532406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6765128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66324.89447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92415208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.236155
X-RAY DIFFRACTIONr_chiral_restr0.0840.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02204
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 32 -
Rwork0.311 669 -
all-701 -
obs--100 %

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