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- PDB-3eji: Crystal structure of Staphylococcal nuclease variant Delta+PHS L3... -

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Basic information

Entry
Database: PDB / ID: 3eji
TitleCrystal structure of Staphylococcal nuclease variant Delta+PHS L36K at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / Calcium / Endonuclease / Metal-binding / Nuclease / Secreted / Zymogen
Function / homology
Function and homology information


endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / endonuclease activity / nucleic acid binding / extracellular region / membrane / metal ion binding
Similarity search - Function
Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / 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) ...Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / 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 / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsKhangulov, V.S. / Schlessman, J.L. / Garcia-Moreno, E.B. / Benning, M. / Isom, D.
CitationJournal: To be Published
Title: Structural Consequences of the Ionization of Lysines at 25 Internal Positions in a Protein
Authors: Chimenti, M.S. / Khangulov, V.S. / Robinson, A.C. / Majumdar, A. / Schlessman, J.L. / Garcia-Moreno, E.B.
History
DepositionSep 18, 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 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 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 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)16,3733
Polymers16,1591
Non-polymers2132
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)48.200, 48.200, 63.210
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: 16159.484 Da / Num. of mol.: 1 / Fragment: UNP residues 80-228 / Mutation: L36K, G50F, V51N, P117G, H124L, S128A, Del44-49
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc, SAR0847 / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6GIK1, UniProt: P00644*PLUS, micrococcal nuclease
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / 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.: 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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 44% MPD, 25 mM Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: BRUKER PROTEUM / Detector: CCD / Date: Jan 22, 2005 / Details: multi-layer optics
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→48.2 Å / Num. all: 11270 / Num. obs: 11208 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.11 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.0344 / Rsym value: 0.0431 / Net I/σ(I): 19.93
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 5.11 % / Rmerge(I) obs: 0.2572 / Mean I/σ(I) obs: 3.75 / Num. unique all: 1736 / Rsym value: 0.2657 / % possible all: 96.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.2 Å
Translation2.5 Å48.2 Å

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
PROTEUM PLUSPLUSdata collection
APEXdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.22 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.271 / WRfactor Rwork: 0.204 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.803 / SU B: 4.437 / SU ML: 0.131 / SU R Cruickshank DPI: 0.213 / SU Rfree: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.272 983 9.8 %RANDOM
Rwork0.203 ---
obs0.209 9990 87.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.76 Å2 / Biso mean: 26.508 Å2 / Biso min: 11.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.37 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1063 0 5 79 1147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221096
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9851472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0895135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8724.79248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67715221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.844155
X-RAY DIFFRACTIONr_chiral_restr0.0990.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02797
X-RAY DIFFRACTIONr_nbd_refined0.210.2518
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2742
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.271
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.29
X-RAY DIFFRACTIONr_mcbond_it0.8831.5672
X-RAY DIFFRACTIONr_mcangle_it1.39521052
X-RAY DIFFRACTIONr_scbond_it2.2673475
X-RAY DIFFRACTIONr_scangle_it3.424.5418
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 32 -
Rwork0.243 297 -
all-329 -
obs--38.71 %

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