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- PDB-1eqv: SIMPLIFICATION OF A PROTEIN LOOP IN STAPHYLOCOCCAL NUCLEASE -

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Basic information

Entry
Database: PDB / ID: 1eqv
TitleSIMPLIFICATION OF A PROTEIN LOOP IN STAPHYLOCOCCAL NUCLEASE
ComponentsTHERMONUCLEASEMicrococcal nuclease
KeywordsHYDROLASE / Protein Engineering / Cis peptide / Cis - trans isomerization
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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.94 Å
AuthorsHodel, A. / Harkins, P.C. / Adelman, D.M. / White, M.A. / Fox, R.O.
Citation
Journal: To be Published
Title: Simplification of a Protein Loop in Staphylococcal Nuclease
Authors: Hodel, A. / Harkins, P.C. / Adelman, D.M. / White, M.A. / Fox, R.O.
#1: Journal: Proteins / Year: 1991
Title: The Crystal Structure of Staphylococcal Nuclease Refined to 1.7 A Resolution
Authors: Hynes, T.R. / Fox, R.O.
History
DepositionApr 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THERMONUCLEASE


Theoretical massNumber of molelcules
Total (without water)15,2671
Polymers15,2671
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.390, 47.390, 62.750
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
2: Residue 38 peptide backbone flipped - Possible error in WT

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Components

#1: Protein THERMONUCLEASE / Micrococcal nuclease


Mass: 15266.704 Da / Num. of mol.: 1 / Mutation: Y113A, V114A, Y115A, K116A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: FOGGI / Production host: Escherichia coli (E. coli) / References: UniProt: P00644, micrococcal nuclease
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 8.15
Details: 10.5 mM potassium phosphate, MPD, pH 8.15, SMALL TUBES, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12781
22781
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
Detector
TypeIDDetectorDate
MACSCIENCE1IMAGE PLATEDec 1, 1994
SDMS2AREA DETECTORDec 2, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→6 Å / Num. all: 9988 / Num. obs: 8600 / % possible obs: 86.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.074
Reflection shellResolution: 1.94→2.06 Å / Num. unique all: 1170 / % possible all: 70

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.94→6 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rwork0.192 --
all0.192 9988 -
obs0.192 8600 86.1 %
Rfree-0 -
Refinement stepCycle: LAST / Resolution: 1.94→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1072 0 0 38 1110
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d24.2
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_improper_angle_d1.41

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