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- PDB-2rdf: Crystal Structure of staphyloccocal nuclease VIAGAN/E75A variant ... -

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Basic information

Entry
Database: PDB / ID: 2rdf
TitleCrystal Structure of staphyloccocal nuclease VIAGAN/E75A variant at cryogenic temperature
ComponentsThermonuclease
KeywordsHYDROLASE / staphylococcal nuclease / long-range interactions / histidine / hyperstable variant / Calcium / Endonuclease / Membrane / Metal-binding / Secreted / Zymogen
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
PHOSPHATE ION / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.01 Å
AuthorsBaran, K. / 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
DepositionSep 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 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)16,8172
Polymers16,7221
Non-polymers951
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.564, 48.564, 63.221
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: 16722.326 Da / Num. of mol.: 1 / Fragment: Nuclease A / Mutation: E75A,D21N,T33V,T41I,S59A,P117G,S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Production host: Escherichia coli (E. coli) / Strain (production host): AR140 / 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.: 72 / 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: 44.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 37% MPD, 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 RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 20, 2004
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 9870 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 30.8 Å2 / Rsym value: 0.037 / Net I/σ(I): 25.7
Reflection shellResolution: 2.01→2.08 Å / Mean I/σ(I) obs: 13.1 / Rsym value: 0.144 / % possible all: 0.998

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementStarting model: 1EZ6 in which all waters were removed, all B's set to 20.00 A^2, and E75A

1ez6


Resolution: 2.01→48.6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1013 10.3 %random
Rwork0.218 ---
all0.232 9845 --
obs0.232 9743 99 %-
Solvent computationBsol: 51.175 Å2
Displacement parametersBiso mean: 32.436 Å2
Baniso -1Baniso -2Baniso -3
1--4.216 Å20 Å20 Å2
2---4.216 Å20 Å2
3---8.432 Å2
Refinement stepCycle: LAST / Resolution: 2.01→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 5 72 1071
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4571.5
X-RAY DIFFRACTIONc_scbond_it2.1772
X-RAY DIFFRACTIONc_mcangle_it2.3032
X-RAY DIFFRACTIONc_scangle_it3.3592.5
LS refinement shellResolution: 2.01→2.04 Å
RfactorNum. reflection% reflection
Rfree0.319 51 -
Rwork0.262 --
obs-481 99 %
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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