7EH3 | pdb_00007eh3

Structure of Nanobody Nb23 in solution using NMR spectroscopy


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride95% H2O/5% D2O21 (sodium chloride) mM6.951 atm298Bruker AVANCE III 600
22D 1H-15N TROSY290 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O95% H2O/5% D2O0 mM6.951 atm298Bruker AVANCE III 600
33D CBCANH250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride95% H2O/5% D2O21 (sodium chloride) mM6.951 atm298Bruker AVANCE III 600
43D CBCA(CO)NH250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride95% H2O/5% D2O21 (sodium chloride) mM6.951 atm298Bruker AVANCE III 600
53D HNCA250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride95% H2O/5% D2O21 (sodium chloride) mM6.951 atm298Bruker AVANCE III 600
63D C(CO)NH250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride95% H2O/5% D2O21 (sodium chloride) mM6.951 atm298Bruker AVANCE III 600
73D H(CCO)NH290 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O95% H2O/5% D2O0 mM6.951 atm298Bruker AVANCE III 600
83D HBHA(CO)NH250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride95% H2O/5% D2O21 (sodium chloride) mM6.951 atm298Bruker AVANCE III 600
93D HNCO250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride95% H2O/5% D2O21 (sodium chloride) mM6.951 atm298Bruker AVANCE III 600
103D HN(CA)CO250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride95% H2O/5% D2O21 (sodium chloride) mM6.951 atm298Bruker AVANCE III 600
112D 1H-1H TOCSY190 uM Nb23, 10 mM sodium phosphate, 5 % D2O, 6.3 mM sodium chloride95% H2O/5% D2O6.3 mM6.951 atm298Bruker AVANCE III 600
123D 1H-15N NOESY290 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O95% H2O/5% D2O0 mM6.951 atm298Bruker AVANCE III 600
132D HBCBCGCDHD190 uM Nb23, 10 mM sodium phosphate, 100 % D2O100% D2O0 mM6.951 atm298Bruker AVANCE III 600
142D HBCBCGCDCEHE190 uM Nb23, 10 mM sodium phosphate, 100 % D2O100% D2O0 mM6.951 atm298Bruker AVANCE III 600
152D 1H-1H NOESY100 uM Nb23, 10 mM sodium phosphate, 100 % D2O, 20 mM sodium chloride100% D2O20 mM6.951 atm298Bruker AVANCE III 600
163D 1H-13C NOESY aliphatic190 uM Nb23, 10 mM sodium phosphate, 100 % D2O100% D2O0 mM6.951 atm298Bruker AVANCE III 600
173D 1H-13C NOESY aromatic190 uM Nb23, 10 mM sodium phosphate, 100 % D2O100% D2O0 mM6.951 atm298Bruker AVANCE III 600
182D 1H-13C HSQC290 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O95% H2O/5% D2O0 mM6.951 atm298Bruker AVANCE III 600
192D 1H-15N HSQC190 uM Nb23, 10 mM sodium phosphate, 100 % D2O100% D2O0 mM6.951 atm298Bruker AVANCE III 600
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE III600
NMR Refinement
MethodDetailsSoftware
energy minimizationNAMD
NMR Ensemble Information
Conformer Selection Criteriastructures with the least restraint violations
Conformers Calculated Total Number20
Conformers Submitted Total Number10
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionTopSpinBruker Biospin
2peak pickingNMRFAM-SPARKYLee W, Tonelli M, Markley JL
3chemical shift assignmentNMRFAM-SPARKYLee W, Tonelli M, Markley JL
4data analysisNMRFAM-SPARKYLee W, Tonelli M, Markley JL
5chemical shift calculationNMRFAM-SPARKYLee W, Tonelli M, Markley JL
6structure calculationCS-ROSETTAShen, Vernon, Baker and Bax
7geometry optimizationMolProbityRichardson
8data analysisMolProbityRichardson
9data analysisPONDEROSALee W, Kim JH, Westler WM, Markley JL
10refinementPONDEROSALee W, Kim JH, Westler WM, Markley JL
11structure calculationPONDEROSALee W, Kim JH, Westler WM, Markley JL
12geometry optimizationPONDEROSALee W, Kim JH, Westler WM, Markley JL
13refinementPONDEROSA-C/SLee W, Stark JL, Markley JL
14structure calculationPONDEROSA-C/SLee W, Stark JL, Markley JL
15geometry optimizationPROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thornton
18geometry optimizationPyMOLThe PyMOL Molecular Graphics System, Version 2.0 Schrodinger, LLC
17data analysisPyMOLThe PyMOL Molecular Graphics System, Version 2.0 Schrodinger, LLC
16data analysisPROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thornton
19geometry optimizationTALOS-NYang S, Bax A
20processingTopSpinBruker Biospin
21data analysisTopSpinBruker Biospin
22refinementNAMDNAMD2Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shi- nozaki A, Varadarajan K, Schulten K