2KA3
Structure of EMILIN-1 C1Q-like domain
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D 15N-NOESY-HSQC | 0.6mM [U-100% 13C; U-100% 15N; 80% 2H] C1q, 20mM phosphate buffer, 100mM sodium chloride, 0.02% NaN3 | 95% H2O/5% D2O | 0.15 | 7.5 | ambient | 310 | |
2 | IPAP 1H,15N-HSQC | 0.6mM [U-100% 13C; U-100% 15N; 80% 2H] C1q, 20mM phosphate buffer, 100mM sodium chloride, 0.02% NaN3, in polyacrylamide gel (Acrylamide:bisacrylamide=4%:3%) | 95% H2O/5% D2O | 0.15 | 7.5 | ambient | 310 | |
3 | TROSY 1H-15N HSQC | 0.6mM [U-100% 13C; U-100% 15N; 80% 2H] C1q, 20mM phosphate buffer, 100mM sodium chloride, 0.02% NaN3, in polyacrylamide gel (Acrylamide:bisacrylamide=4%:3%) | 95% H2O/5% D2O | 0.15 | 7.5 | ambient | 310 | |
4 | 3D HNCO | 0.6mM [U-100% 13C; U-100% 15N; 80% 2H] C1q, 20mM phosphate buffer, 100mM sodium chloride, 0.02% NaN3, in polyacrylamide gel (Acrylamide:bisacrylamide=4%:3%) | 95% H2O/5% D2O | 0.15 | 7.5 | ambient | 310 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | GE | OMEGA | 500 |
2 | GE | OMEGA | 600 |
3 | GE | OMEGA | 750 |
4 | Bruker | AVANCE | 500 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing, restrained energy minimization | The structure was obtained as the refinement of the homology model of emilin trimer C1q-domain based on the chain A of ACRP-30 crystal structure. The quaternary structure of C1q-domain homology model was built with a three-fold simmetry axis. The region between Tyr927 and Gly945 was not modelled and was not included in the refinement. Dihedral angles (obtained with TALOS), RDC values, NOE constraints were used in the refinement procedure. The structures were further refined in order to improve the quality of backbone geometry. For this purpose 2,000 steps of restrained energy minimization were performed using the program NAMD (Kale et al. 1999). The forcefield used is CHARMM v.27b (MacKerell et al. 1998) with the CMAP correction (MacKerell et al., 2004). Since the program does not readily incorporate RDC derived restraints, the z co-ordinates of the backbone amide N and H atoms were restrained at their starting values. Only NOE derived restraints and chemical-shift-derived dihedral angle restraints (with unequivocal secondary structure definition) were imposed. | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 2.0 | Bruker Biospin |
2 | data analysis | Felix | 2.3 | Accelrys Software Inc. |
3 | data analysis | XEASY | 1.2 | Bartels et al. |
4 | data analysis | Sparky | 3.106 | Goddard |
5 | refinement | X-PLOR | 2.9.9 | Brunger |
6 | refinement | NAMD | 2.6b2 | Schulten et al. |