2K9Z

NMR structure of the protein TM1112

Summary for 2K9Z

• Entry DOI: 10.2210/pdb2k9z/pdb
• NMR Information: BMRB: 16006
• Descriptor: uncharacterized protein TM1112 (1 entity in total)
• Functional Keywords: thermotoga maritima, tm1112, structural genomics, psi-2, protein structure initiative, joint center for structural genomics, jcsg, unknown function
• Biological source: Thermotoga maritima
• Total number of polymer chains: 1
• Total formula weight: 10774.42

Authors

Mohanty, B.,Pedrini, B.,Serrano, P.,Geralt, M.,Horst, R.,Herrmann, T.,Wilson, I.A.,Wuthrich, K.,Joint Center for Structural Genomics (JCSG) (deposition date: 2008-10-28, release date: 2008-11-25, Last modification date: 2024-05-08)

Primary citation

Mohanty, B.,Serrano, P.,Pedrini, B.,Jaudzems, K.,Geralt, M.,Horst, R.,Herrmann, T.,Elsliger, M.A.,Wilson, I.A.,Wuthrich, K.
Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
Acta Crystallogr.,Sect.F, 66:1381-1392, 2010

PubMed Abstract: The NMR structures of the TM1112 and TM1367 proteins from Thermotoga maritima in solution at 298 K were determined following a new protocol which uses the software package UNIO for extensive automation. The results obtained with this novel procedure were evaluated by comparison with the crystal structures solved by the JCSG at 100 K to 1.83 and 1.90 Å resolution, respectively. In addition, the TM1112 solution structure was compared with an NMR structure solved by the NESG using a conventional largely interactive methodology. For both proteins, the newly determined NMR structure could be superimposed with the crystal structure with r.m.s.d. values of <1.0 Å for the backbone heavy atoms, which provided a starting platform to investigate local structure variations, which may arise from either the methods used or from the different chemical environments in solution and in the crystal. Thereby, these comparative studies were further explored with the use of reference NMR and crystal structures, which were computed using the NMR software with input of upper-limit distance constraints derived from the molecular models that represent the results of structure determination by NMR and by X-ray diffraction, respectively. The results thus obtained show that NMR structure calculations with the new automated UNIO software used by the JCSG compare favorably with those from a more labor-intensive and time-intensive interactive procedure. An intriguing observation is that the `bundles' of two TM1112 or three TM1367 molecules in the asymmetric unit of the crystal structures mimic the behavior of the bundles of 20 conformers used to represent the NMR solution structures when comparing global r.m.s.d. values calculated either for the polypeptide backbone, the core residues with solvent accessibility below 15% or all heavy atoms.

PubMed: 20944235
DOI: 10.1107/S1744309110020956

Experimental method

SOLUTION NMR