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- PDB-1sty: THE ALPHA ANEURISM: A STRUCTURAL MOTIF REVEALED IN AN INSERTION M... -

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Basic information

Entry
Database: PDB / ID: 1sty
TitleTHE ALPHA ANEURISM: A STRUCTURAL MOTIF REVEALED IN AN INSERTION MUTANT OF STAPHYLOCOCCAL NUCLEASE
ComponentsSTAPHYLOCOCCAL NUCLEASEMicrococcal nuclease
KeywordsHYDROLASE (PHOSPHORIC DIESTER)
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
THYMIDINE-3',5'-DIPHOSPHATE / Thermonuclease
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.67 Å
AuthorsKeefe, L.J. / Lattman, E.E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: The alpha aneurism: a structural motif revealed in an insertion mutant of staphylococcal nuclease.
Authors: Keefe, L.J. / Sondek, J. / Shortle, D. / Lattman, E.E.
#1: Journal: J.Appl.Crystallogr. / Year: 1992
Title: Resolution of a Protein Sequence Ambiguity by X-Ray Crystallographic and Mass Spectrometric Methods
Authors: Keefe, L.J. / Lattman, E.E. / Wolkow, C. / Woods, A. / Chevrier, M. / Cotter, R.J.
History
DepositionFeb 18, 1993Processing site: BNL
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX THE ALPHA ANEURISM IS A UNIQUE BULGE IN AN ALPHA HELIX WHICH OCCURS AT THE INSERTION SITE OF ...HELIX THE ALPHA ANEURISM IS A UNIQUE BULGE IN AN ALPHA HELIX WHICH OCCURS AT THE INSERTION SITE OF THE GLYCINE RESIDUE (IN THE C-TERMINAL ALPHA HELIX BETWEEN RESIDUES ARG 126 AND LYS 127).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STAPHYLOCOCCAL NUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3433
Polymers16,9001
Non-polymers4422
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.952, 46.952, 62.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Atom site foot note2: RESIDUE PRO 117 IS A CIS PROLINE.

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Components

#1: Protein STAPHYLOCOCCAL NUCLEASE / Micrococcal nuclease


Mass: 16900.381 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: 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 / Thymidine diphosphate


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


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal grow
*PLUS
Temperature: 7 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
450-70 %MPD1reservoir
1protein1drop
2calcium chloride1reservoir
3thymidine 3', 5'-bisphosphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.67 Å / Num. obs: 13012 / % possible obs: 87.8 % / Observed criterion σ(F): 2 / Num. measured all: 42377 / Rmerge(I) obs: 0.0502

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.17 / Highest resolution: 1.67 Å
Refinement stepCycle: LAST / Highest resolution: 1.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 26 147 1279
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg2.67
Software
*PLUS
Name: X-PLOR/PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d2.67
X-RAY DIFFRACTIONp_dihedral_angle_d24.6
X-RAY DIFFRACTIONp_dihedral_angle_deg1.08

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