Mass: 7805.653 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 Description: The protein is a monomer by gel filtration chromatography and static light scattering. Gene: VP1593 / Plasmid: VpR55-21.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q87PC4
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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 1H-13C 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
3DHBHA(CO)NH
1
10
1
3DC(CO)NH
1
11
1
3D (H)CCH-TOCSY
1
12
1
3D CCH-TOCSY
1
13
2
2D 1H-13C HSQC high resolution
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1.1 mM [U-100% 13C; U-100% 15N] VpR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O
95% H2O/5% D2O
2
1.1 mM [U-5% 13C; U-100% 15N] VpR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O
Method: simulated annealing / Software ordinal: 10 Details: THE STRUCTURES ARE BASED ON A TOTAL OF 865 COMFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 154 DIHEDRAL ANGLE CONSTRAINTS, AND 50 HYDROGEN BOND CONSTRAINTS (18.4 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 865 COMFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 154 DIHEDRAL ANGLE CONSTRAINTS, AND 50 HYDROGEN BOND CONSTRAINTS (18.4 CONSTRAINTS PER RESIDUE, 2.8 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 60 BY PSVS 1.3) STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM AUTOSTRUCTURE. THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE C-TERMINAL HIS TAG RESDIUES OF THE PROTEIN (HHHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED(S(PHI)+S(PSI)<1.8): 1-4, 54-60. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND THE SIDE CHAIN ASSIGNMENTS WERE CO PLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE, HIHEDRAL ANGLE (HYPER) AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENT (EXCLUDING C-TERMINAL HHHHH): BACKBONE,99.66%, SIDE CHAIN, 92.20%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE 1-60 PSVS 1.3), WHERE ORDERED RESIDUES (S(PHI)+S(PSI)>1.8) COMPRISE: 5-54. (A) RMSD (ORDERED RESIDUES): BB 0.5, HEAVY ATOM: 1.2 (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 83.6%, ADDITIONALLY ALLOWED: 13.8%, GENEROUSLY ALLOWED : 0.2%, DISALLOWED,2.3%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): PHI-PSI, -0.14/-0.24, ALL , -0.16/-0.95. (D) MOLPROBITY CLASH SCORE (RAW/Z): 19.25/-1.78. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUE 1-60): RECALL, 0.962, PRECISION, 0.921, F-MEASURE, 0.941, DP-SCORE, 0.804.
NMR constraints
NOE constraints total: 865 / NOE intraresidue total count: 171 / NOE long range total count: 164 / NOE medium range total count: 277 / NOE sequential total count: 253
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 torsion angle constraint violation: 4.9 ° / Maximum upper distance constraint violation: 0.45 Å
NMR ensemble rms
Distance rms dev: 0.02 Å
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