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- PDB-1syc: ENGINEERING ALTERNATIVE BETA-TURN TYPES IN STAPHYLOCOCCAL NUCLEASE -

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Basic information

Entry
Database: PDB / ID: 1syc
TitleENGINEERING ALTERNATIVE BETA-TURN TYPES IN STAPHYLOCOCCAL NUCLEASE
ComponentsSTAPHYLOCOCCAL NUCLEASE
KeywordsHYDROLASE(PHOSPHORIC DIESTER)
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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsHynes, T.R. / Hodel, A. / Fox, R.O.
Citation
Journal: Biochemistry / Year: 1994
Title: Engineering alternative beta-turn types in staphylococcal nuclease.
Authors: Hynes, T.R. / Hodel, A. / Fox, R.O.
#1: Journal: Proteins / Year: 1991
Title: The Crystal Structure of Staphylococcal Nuclease Refined at 1.7 Angstroms Resolution
Authors: Hynes, T.R. / Fox, R.O.
#2: 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
DepositionJan 7, 1994Processing 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 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)16,8031
Polymers16,8031
Non-polymers00
Water1,24369
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

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Components

#1: Protein STAPHYLOCOCCAL NUCLEASE


Mass: 16803.268 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.: 69 / 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: 44.63 %
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8.15 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.5 mMpotassium phosphate1drop
22 mg/mLprotein1drop
325 %MPD1drop

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. obs: 20238 / % possible obs: 59 % / Num. measured all: 33206 / Rmerge(I) obs: 0.013

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→8 Å / Rfactor obs: 0.182 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 0 69 1157
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.016
X-RAY DIFFRACTIONp_angle_d0.0350.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.036
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0150.015
X-RAY DIFFRACTIONp_chiral_restr0.1790.179
X-RAY DIFFRACTIONp_singtor_nbd0.1640.164
X-RAY DIFFRACTIONp_multtor_nbd0.1580.158
X-RAY DIFFRACTIONp_xhyhbond_nbd0.160.16
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.82.8
X-RAY DIFFRACTIONp_staggered_tor18.718.7
X-RAY DIFFRACTIONp_orthonormal_tor2020
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr

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