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- PDB-3d8g: Crystal structure of Staphylococcal nuclease variant Delta+PHS I7... -

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Basic information

Entry
Database: PDB / ID: 3d8g
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS I72R at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / internal arg / Endonuclease / Metal-binding / Nuclease / Secreted / Zymogen
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 / 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
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus MW2 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å
AuthorsHarms, M.J. / Schlessman, J.L. / Garcia-Moreno, E.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Arginine residues at internal positions in a protein are always charged.
Authors: Harms, M.J. / Schlessman, J.L. / Sue, G.R. / Garcia-Moreno E, B.
History
DepositionMay 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Dec 14, 2011Group: Database references
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 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

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Assembly

Deposited unit
A: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6303
Polymers16,1881
Non-polymers4422
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.181, 60.425, 73.124
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 16187.500 Da / Num. of mol.: 1 / Fragment: UNP database residues 80-228 / Mutation: G50F, V51N, I72R, P117G, H124L, S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus MW2 (bacteria)
Gene: nuc, MW0769 / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NXI6, micrococcal nuclease
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-THP / THYMIDINE-3',5'-DIPHOSPHATE


Type: DNA linking / Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: BRUKER APEX II / Detector: CCD / Date: Jun 13, 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
ReflectionResolution: 1.99→46.6 Å / Num. all: 10315 / Num. obs: 10279 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.75 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.0215 / Rsym value: 0.0581 / Net I/σ(I): 42.54
Reflection shellResolution: 1.99→2.09 Å / Redundancy: 9.35 % / Rmerge(I) obs: 0.0965 / Mean I/σ(I) obs: 9.87 / Num. unique all: 1358 / Rsym value: 0.2078 / % possible all: 97.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.58 Å
Translation2.5 Å46.58 Å

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
APEXdata collection
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RCSB entry 1tqo, all waters removed, b = 20.0, ILE-72 and ILE-92 truncated to ALA

1tqo


Resolution: 1.99→1.99 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.895 / SU B: 3.798 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.208 / ESU R Free: 0.189 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1019 10 %RANDOM
Rwork0.2 ---
all0.205 10280 --
obs0.205 10218 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.049 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.99→1.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 26 87 1158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221089
X-RAY DIFFRACTIONr_angle_refined_deg1.2262.0041464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6475129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07224.69449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56315211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.517156
X-RAY DIFFRACTIONr_chiral_restr0.0780.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02794
X-RAY DIFFRACTIONr_nbd_refined0.2030.2437
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.27
X-RAY DIFFRACTIONr_mcbond_it0.6411.5671
X-RAY DIFFRACTIONr_mcangle_it0.95121028
X-RAY DIFFRACTIONr_scbond_it1.4193489
X-RAY DIFFRACTIONr_scangle_it2.2484.5436
LS refinement shellResolution: 1.99→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 62 -
Rwork0.187 646 -
all-708 -
obs--94.91 %

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