2KL7
Solution NMR Structure of the EGF-like 1 Domain of Human Fibulin-4. Northeast Structural Genomics Target HR6275
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
2 | 2D 1H-13C HSQC | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
3 | 3D CBCA(CO)NH | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
4 | 3D HNCACB | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
5 | 3D HNCO | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
6 | 3D HBHA(CO)NH | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
7 | 3D HN(CA)CO | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
8 | 3D 1H-15N NOESY | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
9 | 3D 1H-13C NOESY | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
10 | 3D HCCH-TOCSY | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
11 | 3D HCCH-COSY | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
12 | 3D CCH-TOCSY | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
13 | 2D 1H-15N HMQC | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
14 | 2D 1H-15N het_NOE | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
15 | 1D 15N_T1 series | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
16 | 1D 15N_T2 series | 0.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
17 | 2D 1H-15N HSQC | 0.3 mM [U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
2 | Bruker | AVANCE | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
molecular dynamics | NOESY ASSIGNMENTS BY CYANA-3.0. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA-3.0. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). STRUCTURE BASED ON 776 NOE, 106 DIHE. MAX NOE VIOLATION: 0.23 A (1MODEL); MAX DIHE VIOLATION: 7.1 DEG. 1 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES: 11-34,53-66 (FINDCORE). SECONDARY STRUCTURE - BETA STRANDS: 17-21, 25-29, 61-63. RMSD(ANG): BACKBONE 1.0, ALL HEAVY ATOMS 1.3. RAMA. DISTRIBUTION: 94.1/5.9/0.0/0.0. PROCHECK (PSI-PHI): -0.38/-1.18 (RAW/Z), PROCHECK (ALL): -0.22/-1.30 (RAW/Z), MOLPROBITY CLASH: 16.14/-1.24 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.880, PRECISION: 0.916, F-MEASURE: 0.898, DP-SCORE: 0.651. | CYANA |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
---|---|
Details | MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2(CPMG) T1=664.9 MS T2=128.48 MS TAUC=4.8 NS. CONSISTENT WITH MOLECULAR WEIGHT OF MONOMERIC UNIT. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. ASSIGNMENT STATS (ALL RESIDUES INCLUDED): BACKBONE 91.89%, SIDECHAIN 83.74%, AROMATIC (SC) 100%. UNAMBIGUOUS SIDECHAIN NH2 100%. |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | structure solution | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
2 | refinement | CNS | 1.3 | Brunger, Adams, Clore, Gros, Nilges and Read |
3 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
4 | collection | TopSpin | 2.1 | Bruker Biospin |
5 | validation | PSVS | 1.3 | Bhattacharya and Montelione |
6 | data analysis | Sparky | 2.113 | Goddard |
7 | data analysis | PINE | Bahrami, Markley, Assadi, and Eghbalnia | |
8 | visualization | MOLMOL | Koradi, Billeter and Wuthrich | |
9 | visualization | PyMOL | DeLano Scientific | |
10 | pdb processing | PdbStat | 5.1 | Tejero, Montelione |