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- PDB-2qdb: Crystal structure of staphylococcal nuclease variant E75Q/D21N/T3... -

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Basic information

Entry
Database: PDB / ID: 2qdb
TitleCrystal structure of staphylococcal nuclease variant E75Q/D21N/T33V/T41I/S59A/P117G/S128A at 100 K
ComponentsThermonuclease
KeywordsHYDROLASE / Staphylococcal nuclease / hyperstable variant / NVIAGA
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
PHOSPHATE ION / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBaran, K.L. / Schlessman, J.L. / Garcia-Moreno, B.E.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Electrostatic effects in a network of polar and ionizable groups in staphylococcal nuclease.
Authors: Baran, K.L. / Chimenti, M.S. / Schlessman, J.L. / Fitch, C.A. / Herbst, K.J. / Garcia-Moreno, B.E.
History
DepositionJun 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Aug 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)16,8742
Polymers16,7791
Non-polymers951
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.668, 48.668, 63.277
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: 16779.377 Da / Num. of mol.: 1 / Fragment: Nuclease A / Mutation: E75Q,D21N,T33V,T41I,S59A,P117G,S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: lambda / Production host: Escherichia coli (E. coli) / Strain (production host): AR120 / References: UniProt: P00644, micrococcal nuclease
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 38% MPD and 25 mM potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 5, 2005 / 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: 2.2→48.7 Å / Num. all: 7570 / Num. obs: 7518 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Redundancy: 7 % / Rsym value: 0.066 / Net I/σ(I): 17.4
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 5.2 / Rsym value: 0.233 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
CrystalCleardata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZ6 modified as follows: all variant residues were truncated to Ala, B's were reset to 20.0 A^2, waters were removed

1ez6


Resolution: 2.2→48.7 Å / FOM work R set: 0.778 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 765 10.1 %random
Rwork0.239 ---
all0.255 7570 --
obs0.26 7512 99.3 %-
Solvent computationBsol: 50.743 Å2
Displacement parametersBiso mean: 36.728 Å2
Baniso -1Baniso -2Baniso -3
1--6.548 Å20 Å20 Å2
2---6.548 Å20 Å2
3---13.096 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 0 5 36 1039
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_scbond_it2.2682
X-RAY DIFFRACTIONc_mcangle_it2.3012
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.2-2.250.461460.298441487
2.25-2.310.346440.292467511
2.31-2.370.373490.299438487
2.37-2.440.367470.267452499
2.44-2.520.405560.248444500
2.52-2.610.281510.261446497
2.61-2.710.273490.261437486
2.71-2.840.35430.294466509
2.84-2.990.36450.244440485
2.99-3.170.275500.269461511
3.17-3.420.302600.243438498
3.42-3.760.272430.241474517
3.76-4.310.221580.203440498
4.31-5.420.194610.182451512
5.42-500.276630.256452515
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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