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- PDB-4wor: Staphylococcal nuclease in complex with Ca2+ and thymidine-3'-5'-... -

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Basic information

Entry
Database: PDB / ID: 4wor
TitleStaphylococcal nuclease in complex with Ca2+ and thymidine-3'-5'-diphosphate (pdTp) at room temperature
ComponentsThermonuclease
KeywordsHYDROLASE/HYDROLASE inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.596 Å
AuthorsWall, M.E. / Ealick, S.E. / Gruner, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 1997
Title: Three-dimensional diffuse x-ray scattering from crystals of Staphylococcal nuclease.
Authors: Wall, M.E. / Ealick, S.E. / Gruner, S.M.
History
DepositionOct 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 2.0Sep 20, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.id / _entity_src_gen.pdbx_alt_source_flag ..._atom_site.id / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2863
Polymers16,8431
Non-polymers4422
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-11 kcal/mol
Surface area7060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.499, 48.499, 63.430
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


Mass: 16843.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: pFOG405 / Production host: Escherichia coli (E. coli) / References: UniProt: P00644, micrococcal nuclease
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-THP / THYMIDINE-3',5'-DIPHOSPHATE


Type: DNA linking / Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.46 % / Description: 2.0 mm x 0.4 mm x 0.4 mm rod
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.15
Details: 2-methyl-2,4-pentanediol (MPD), potassium phosphate, thymidine-3',5'-diphosphate (pdTp), Ca2+

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 Å
DetectorType: PRINCETON 2K / Detector: CCD / Date: Feb 17, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.596→24.25 Å / Num. all: 37237 / Num. obs: 19093 / % possible obs: 97.59 % / Redundancy: 2 % / Rmerge(I) obs: 0.07585 / Net I/σ(I): 8.22
Reflection shellResolution: 1.596→1.653 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5368 / Mean I/σ(I) obs: 1.55 / % possible all: 96.06

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1779) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SNC

1snc


Resolution: 1.596→24.249 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 1880 5.13 %Random selection
Rwork0.1799 ---
obs0.1811 36626 95.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.596→24.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 26 79 1142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171085
X-RAY DIFFRACTIONf_angle_d1.2841466
X-RAY DIFFRACTIONf_dihedral_angle_d13.22400
X-RAY DIFFRACTIONf_chiral_restr0.053160
X-RAY DIFFRACTIONf_plane_restr0.006186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5961-1.63920.36251230.32462606X-RAY DIFFRACTION93
1.6392-1.68740.28951480.28422500X-RAY DIFFRACTION90
1.6874-1.74190.29561600.25342632X-RAY DIFFRACTION93
1.7419-1.80410.25761560.23082621X-RAY DIFFRACTION93
1.8041-1.87630.2411620.22252615X-RAY DIFFRACTION94
1.8763-1.96170.23931780.20082633X-RAY DIFFRACTION96
1.9617-2.0650.28591320.18662676X-RAY DIFFRACTION96
2.065-2.19430.17281300.17232762X-RAY DIFFRACTION97
2.1943-2.36360.22231120.17152771X-RAY DIFFRACTION97
2.3636-2.60130.22541400.17452718X-RAY DIFFRACTION97
2.6013-2.97710.20271480.17432738X-RAY DIFFRACTION98
2.9771-3.74860.15921540.15812753X-RAY DIFFRACTION98
3.7486-24.25220.17641370.16622721X-RAY DIFFRACTION97

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