2K04
Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D_15N-separated_NOESY | .31 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .775 mM CXCR4 | 90% H2O/10% D2O | 21 | 6.8 | AMBIENT | 308 | |
2 | 3D_13C-separated_NOESY | .31 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .775 mM CXCR4 | 90% H2O/10% D2O | 21 | 6.8 | AMBIENT | 308 | |
3 | 3D_13C-separated_NOESY (AROMATIC) | .31 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .775 mM CXCR4 | 90% H2O/10% D2O | 21 | 6.8 | AMBIENT | 308 | |
4 | 3D_13C-F1-filtered_13C-F3-separateded_NOESY | .31 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .775 mM CXCR4 | 90% H2O/10% D2O | 21 | 6.8 | AMBIENT | 308 | |
5 | 3D_15N-separated_NOESY | 1.0 mM [U-100% 13C; U-100% 15N] CXCR4, 0.625 mM CXCL12/SDF1-alpha | 90% H2O/10% D2O | 21 | 6.8 | AMBIENT | 308 | |
6 | 3D_13C-separated_NOESY | 1.0 mM [U-100% 13C; U-100% 15N] CXCR4, 0.625 mM CXCL12/SDF1-alpha | 90% H2O/10% D2O | 21 | 6.8 | AMBIENT | 308 | |
7 | 3D_13C-separated_NOESY (AROMATIC) | 1.0 mM [U-100% 13C; U-100% 15N] CXCR4, 0.625 mM CXCL12/SDF1-alpha | 90% H2O/10% D2O | 21 | 6.8 | AMBIENT | 308 | |
8 | 3D_13C-F1-filtered_13C-F3-separateded_NOESY | 1.0 mM [U-100% 13C; U-100% 15N] CXCR4, 0.625 mM CXCL12/SDF1-alpha | 90% H2O/10% D2O | 21 | 6.8 | AMBIENT | 308 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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Method | Details | Software |
AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. | CXCL12/CXCR4 COMPLEX STRUCTURES ARE BASED ON A TOTAL OF 2012 NOE CONSTRAINTS ( 744 INTRA, 384 SEQUENTIAL, 238 MEDIUM, 444 LONG RANGE, 110 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND 92 INTERMOLECULAR CONSTRAINTS (CXCL12 TO CXCR4)) AND 128 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINT WERE IN ONE ASSIGNED AND VALIDATED IN ONE CXCL12/CXCR4 COMPLEX AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINT IN THE SECOND COMPLEX. CONSTRAINT TOTALS LISTED ABOVE INCLUDE CONSTRAINTS FROM BOTH MONOMERS. | Xplor-NIH |
NMR Ensemble Information | |
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Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Xplor-NIH | 2.9.3 | SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M. |
2 | collection | XwinNMR | 3.5 | Bruker |
3 | processing | NMRPipe | 2004 | Delagio,F. et al. |
4 | data analysis | XEASY | 1.3 | Eccles, C., Guntert, P., Billeter, M., Wuthrich, K. |
5 | data analysis | SPSCAN | 1.1.0 | R.W. Glaser |
6 | data analysis | GARANT | 2.1 | C. Bartels |
7 | structural calculation | CYANA | 2.1 | Guntert, P. |