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- PDB-4h7b: Crystal Structure of Staphylococcal nuclease mutant I72V/V99L -

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Basic information

Entry
Database: PDB / ID: 4h7b
TitleCrystal Structure of Staphylococcal nuclease mutant I72V/V99L
ComponentsThermonuclease
KeywordsHYDROLASE / DNA hydrolase / RNA hydrolase / endonuclease
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 / membrane / 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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSanders, J.M. / Janowska, K. / Sakon, J. / Stites, W.E.
CitationJournal: To be Published
Title: Hydrophobic core mutants of Staphylococcal nuclease
Authors: Sanders, J.M. / Janowska, K. / Sakon, J. / Stites, W.E.
History
DepositionSep 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Thermonuclease


Theoretical massNumber of molelcules
Total (without water)16,8431
Polymers16,8431
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.454, 47.454, 63.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 16843.330 Da / Num. of mol.: 1 / Fragment: UNP Residues 83-231 / Mutation: I72V, V99L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: pL13 / Production host: Escherichia coli (E. coli) / Strain (production host): Ar120 / References: UniProt: P00644, micrococcal nuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25mM Sodium Phosphate buffer, 35-60% MPD, Vapor Diffusion, Hanging Drop, Temperature 277K, pH 7.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→21.22 Å / Num. obs: 14927

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CCP4model building
REFMAC5.5.0109refinement
d*TREKdata reduction
d*TREKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→21.22 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.086 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24836 797 5.1 %RANDOM
Rwork0.19215 ---
obs0.19498 14927 84.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.763 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→21.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 0 65 1156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221139
X-RAY DIFFRACTIONr_angle_refined_deg2.1421.981526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6915135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9624.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.93215236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.763156
X-RAY DIFFRACTIONr_chiral_restr0.1560.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021825
X-RAY DIFFRACTIONr_mcbond_it1.4311.5678
X-RAY DIFFRACTIONr_mcangle_it2.70821094
X-RAY DIFFRACTIONr_scbond_it4.2253461
X-RAY DIFFRACTIONr_scangle_it7.0244.5432
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.67 9 -
Rwork0.467 210 -
obs--15.96 %

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