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- PDB-1stn: THE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE REFINED AT 1.7 A... -

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Entry
Database: PDB / ID: 1stn
TitleTHE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE REFINED AT 1.7 ANGSTROMS RESOLUTION
ComponentsSTAPHYLOCOCCAL NUCLEASE
KeywordsHYDROLASE(PHOSPHORIC DIESTER)
Function / homology
Function and homology information


micrococcal nuclease / : / nucleic acid binding / extracellular region / metal ion binding / membrane
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 / Resolution: 1.7 Å
AuthorsHynes, T.R. / Fox, R.O.
Citation
Journal: Proteins / Year: 1991
Title: The crystal structure of staphylococcal nuclease refined at 1.7 A resolution.
Authors: Hynes, T.R. / Fox, R.O.
#1: Journal: Nature / Year: 1989
Title: Transfer of a Beta-Turn Structure to a New Protein Context
Authors: Hynes, T.R. / Kautz, R.A. / Goodman, M.A. / Gill, J.F. / Fox, R.O.
History
DepositionFeb 17, 1993Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STAPHYLOCOCCAL NUCLEASE


Theoretical massNumber of molelcules
Total (without water)16,8431
Polymers16,8431
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.500, 48.500, 63.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Atom site foot note1: CIS PROLINE - PRO 117

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Components

#1: Protein STAPHYLOCOCCAL NUCLEASE


Mass: 16843.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / References: UniProt: P00644, micrococcal nuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8.15 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 %(w/w)MPD1reservoir
210.5 mMpotasssium phosphate1reservoir
32 mg/mlnuclease1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 14893 / % possible obs: 93 % / Num. measured all: 38517 / Rmerge(I) obs: 0.051

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.7→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.162 -
obs0.162 12359
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 0 83 1174
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it11.2
X-RAY DIFFRACTIONx_mcangle_it1.71.8
X-RAY DIFFRACTIONx_scbond_it5.54
X-RAY DIFFRACTIONx_scangle_it8.46
Refinement
*PLUS
Rfactor obs: 0.162 / Rfactor Rwork: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.46 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.030.033
X-RAY DIFFRACTIONx_planar_d0.030.037
X-RAY DIFFRACTIONx_plane_restr0.020.014
X-RAY DIFFRACTIONx_chiral_restr0.150.178

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