PH-domain like - #80 / Domain of unknown function DUF1508 / Domain of unknown function (DUF1508) / YegP-like superfamily / PH-domain like / Roll / Mainly Beta / UPF0339 protein SO_3888
Mass: 13103.619 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_3888 / Plasmid: SoR190-21.2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EAL4
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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
2D 1H-15N HSQC
1
2
1
2D 1H-13C HSQC
1
3
1
3D 1H-15N NOESY
1
4
1
3D simutaneous NOESY
1
5
1
3D 1H-13C NOESY aromatic
1
6
1
3D HNCO
1
7
1
3D HN(CA)CB
1
8
1
3DCBCA(CO)NH
1
9
1
3D (H)CCH-COSY
1
10
1
3D (H)CCH-TOCSY
1
11
1
3DHBHA(CO)NH
1
12
2
2D 1H-13C HSQC high resolution
1
13
1
3D CCH-TOCSY
NMR details
Text: The protein is a monomer by gel filtration chromatography and static light scattering.
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O
95% H2O/5% D2O
2
1.3 mM [U-5% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O
95% H2O/5% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
1.3mM
SoR190
[U-100% 13C; U-100% 15N]
1
5mM
CaCl2
1
100mM
sodiumchloride
1
20mM
ammoniumacetate
1
10mM
DTT
1
0.02 %
NaN3
1
1.3mM
SoR190
[U-5% 13C; U-100% 15N]
2
5mM
CaCl2
2
100mM
sodiumchloride
2
20mM
ammoniumacetate
2
10mM
DTT
2
0.02 %
NaN3
2
Sample conditions
Ionic strength: 0.1 M / pH: 5.5 / Pressure: ambient / Temperature: 293 K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker Avance
Bruker
AVANCE
800
1
Bruker Avance
Bruker
AVANCE
600
2
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Processing
NMR software
Name
Version
Developer
Classification
TopSpin
2.1
BrukerBiospin
collection
AutoAssign
2.2.1
Zimmerman, Moseley, KulikowskiandMontelione
chemicalshiftassignment
Sparky
3.11
Goddard
peakpicking
Sparky
3.11
Goddard
dataanalysis
AutoStructure
2.2.1
Huang, Tejero, PowersandMontelione
structuresolution
NMRPipe
2.3
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
CYANA
2.1
Guntert, MumenthalerandWuthrich
structuresolution
CNS
1.1
Brunger, Adams, Clore, Gros, NilgesandRead
refinement
PSVS
1.3
BhattacharyaandMontelione
dataanalysis
PdbStat
5
TejeroandMontelione
pdbanalysis
Refinement
Method: simulated annealing / Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2291 COMFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 146 DIHEDRAL ANGLE CONSTRAINTS, AND 92 HYDROGEN BOND CONSTRAINTS (22.4 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2291 COMFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 146 DIHEDRAL ANGLE CONSTRAINTS, AND 92 HYDROGEN BOND CONSTRAINTS (22.4 CONSTRAINTS PER RESIDUE, 7.7 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 118 BY PSVS 1.3) STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE AND CYANA. THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS AND HAVE BEEN INCLUDED IN THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED (S(PHI)+S(PSI)<1.8): 1-3, 21-22, 112-118. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE, DIHEDRAL ANGLE (TALOS) AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING CYANA. COMPLETENESS OF NMR ASSIGNMENT: BACKBONE, 94.10%, SIDE CHAIN, 82.27%, AROMATICS, 76.92%, STEREOSPECIFIC METHYL, 91.67%, FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE 1-118 PSVS 1.3), WHERE ORDERED RESIDUE RANGES (S(PHI)+S(PSI)>1.8) COMPRISE: 4-20, 23-111. (A) RMSD (ORDERED RESIDUES): BB 0.6, HEAVY ATOM: 1.1 (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 88.1%, ADDITIONALLY ALLOWED: 11.8%, GENEROUSLY ALLOWED : 0.1%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): PHI-PSI, -0.30/-0.87, ALL , -0.12/-0.71. (D) MOLPROBITY CLASH SCORE (RAW/Z): 13.32/-0.76. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUE 1-118): RECALL, 1, PRECISION, 0.975, F-MEASURE, 0.987, DP-SCORE, 0.89.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.22 Å
NMR ensemble rms
Distance rms dev: 0.01 Å
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