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- PDB-1u9r: Crystal Structure of Staphylococcal Nuclease mutant V66E/P117G/H1... -

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Basic information

Entry
Database: PDB / ID: 1u9r
TitleCrystal Structure of Staphylococcal Nuclease mutant V66E/P117G/H124L/S128A at Room Temperature
ComponentsThermonucleaseMicrococcal nuclease
KeywordsHYDROLASE / Staphylococcal nuclease / nuclease / hyperstable variant / internal waters
Function / homology
Function and homology information


endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / 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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDenisov, V.P. / Schlessman, J.L. / Garcia-Moreno, B.E. / Halle, B.
CitationJournal: Biophys.J. / Year: 2004
Title: Stabilization of internal charges in a protein: water penetration or conformational change?
Authors: Denisov, V.P. / Schlessman, J.L. / Garcia-Moreno, B.E. / Halle, B.
History
DepositionAug 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)16,7921
Polymers16,7921
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.794, 48.794, 63.788
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 / Micrococcal nuclease / TNase / Micrococcal nuclease / Staphylococcal nuclease


Mass: 16792.260 Da / Num. of mol.: 1 / Mutation: V66E/P117G/H124L/S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: lambda / Cell line (production host): AR120 / Production host: Escherichia coli (E. coli) / References: UniProt: P00644, micrococcal nuclease
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.254 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: MPD, potassium phosphate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 2003 / Details: mirrors
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 8569 / Num. obs: 8569 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 28.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 10 / Num. unique all: 826 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Staphylococcal nuclease V66E/P117G/H124L/S128A low-temperature coordinates

Resolution: 2.1→48.79 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 519402.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 900 10.6 %RANDOM
Rwork0.193 ---
all0.196 8568 --
obs0.193 8484 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.7182 Å2 / ksol: 0.345061 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.62 Å20 Å20 Å2
2--2.62 Å20 Å2
3----5.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 0 32 1062
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it2.522
X-RAY DIFFRACTIONc_scangle_it3.912.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 145 10.9 %
Rwork0.215 1188 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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