- PDB-1jor: Ensemble structures for unligated Staphylococcal nuclease-H124L -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1jor
Title
Ensemble structures for unligated Staphylococcal nuclease-H124L
Components
staphylococcal nuclease
Keywords
HYDROLASE / beta barrel / alpha helix
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 / cytoplasm 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
Mass: 16818.340 Da / Num. of mol.: 1 / Fragment: nuclease A / Mutation: H124L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pTSN2cc / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: P00644, micrococcal nuclease
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
E-COSY
2
2
2
HMQC-J
1
3
3
DQF-COSY
1
4
1
2D NOESY
2
5
4
2D NOESY
2
6
2
3D 1H-15N NOESY-HMQC
2
7
5
2D 1H-13C HMQC
2
8
6
HNCO
2
9
6
3D HNCA
1
10
1
andothers
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
3.5-5 mM Nuclease-H124L U-50% 2H; 300 mM KCl; D2O
D2O
2
3.5-5 mM Nuclease-H124L U-95% 15N; 300 mM KCl; H2O
H2O
3
3.5-5 mM Nuclease-H124L; 300 mM KCl; D2O
D2O
4
3.5-5 mM Nuclease-H124L U-50% 2H; 300 mM KCl; H2O
H2O
5
3.5-5 mM Nuclease-H124L U-98% 13C; 300 mM KCl; H2O
H2O
6
3.5-5 mM Nuclease-H124L U-98% 13C U-99% 15N; 300 mM KCl; H2O
H2O
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
300nMKCl
5.5
ambient
318K
2
300nMKCl
5.1
ambient
318K
Crystal grow
*PLUS
Method: other / Details: NMR
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AM
Bruker
AM
500
1
Bruker AM
Bruker
AM
600
2
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Processing
NMR software
Name
Version
Developer
Classification
Felix
BiosymTechnologiesInc
processing
X-PLOR
3.1
Brunger
structuresolution
Insight II
2.3
BiosymTechnologiesInc
structuresolution
HBPLUS
McDonaldandThornton
structuresolution
X-PLOR
3.1
Brunger
refinement
Refinement
Method: Distance, hydrogen bond, torsion angle constraints / Software ordinal: 1 Details: 2176 constraints were used to calculate the structure
NMR ensemble
Conformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations Conformers calculated total number: 90 / Conformers submitted total number: 30
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