2JQN

Solution NMR structure of CC0527 from Caulobacter crescentus. Northeast Structural Genomics Target CCR55


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
22D 1H-13C HSQC0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
33D 1H-15N NOESY0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
43D 1H-13C NOESY0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
53D 1H-13C NOESY aromatic0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
63D 1H-13C NOESY0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3100% D2O1006.5ambient293
73D HNCO0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
83D HN(CA)CO0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
93D HN(CO)CA0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
103D HNCA0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
113D GFT HNNCACBCA0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
123D GFT CACB(CO)NHN0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
133D GFT HAHBCACB(CO)NHN0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
143D HCCH-TOCSY0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
153D HCCH-COSY0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
163D CCH-TOCSY0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
173D HNHA0.98 mM [U-100% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
182D 1H-13C HSQC high res.0.58 mM [U-5% 13C; U-100% 15N] CcR55, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN395% H2O/5% D2O1006.5ambient293
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianINOVA600
2BrukerAVANCE600
3BrukerAVANCE800
NMR Refinement
MethodDetailsSoftware
simulated annealingTHE STRUCTURES ARE BASED ON A TOTAL OF 1164 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 108 DIHEDRAL ANGLE CONSTRAINTS, AND 66 HYDROGEN BOND CONSTRAINTS (11.7 CONSTRAINTS PER RESIDUE, 3.6 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 116 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).TopSpin
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number100
Conformers Submitted Total Number20
Representative Model1 (lowest energy)
Additional NMR Experimental Information
DetailsTHE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE AND GFT NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE, DIHEDRAL ANGLE (HYPER) AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 97.6%, SIDE CHAIN, 96.5%, AROMATICS, 89.1%, STEREOSPECIFIC METHYL, 91.3%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 116, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 3-22,26-31,34-35,40-49,56-62,69-73,80-96,109-112: (A) RMSD (ORDERED RESIDUES): BB, 0.9, HEAVY ATOM, 1.3. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 91.3%, ADDITIONALLY ALLOWED, 8.7%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.25/-0.67, ALL, -0.15/-0.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 19.99/-1.90. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-116): RECALL, 0.985, PRECISION, 0.900, F-MEASURE, 0.941, DP-SCORE, 0.755. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) 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): 1-2,23-25,32-33,36-39,50-55,63-68,74-79,97-108,113-116.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionTopSpin1.3Bruker Biospin
2chemical shift assignmentAutoAssign2.2.1Zimmerman, Moseley, Kulikowski and Montelione
3peak pickingSparky3.110Goddard
4data analysisSparky3.110Goddard
5structure solutionAutoStructure2.1.1Huang, Tejero, Powers and Montelione
6processingNMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
7structure solutionX-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clore
8refinementX-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clore
9structure solutionCNS1.1Brunger, Adams, Clore, Gros, Nilges and Read
10refinementCNS1.1Brunger, Adams, Clore, Gros, Nilges and Read
11data analysisPSVS1.3Bhattacharya and Montelione
12pdb analysisPdbStat5.0Tejero and Montelione
13collectionVNMR6.1CVarian