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PDB ID Mentions in PubMed Central Article count: 2

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Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit.

(2009) Acta Crystallogr D Biol Crystallogr 65

PubMed: 19564683 | PubMedCentral: PMC2703569 | DOI: 10.1107/S0907444909010695

Structure of the CorA Mg 2+ transporter at 3.9 Å resolution The reported structure of the CorA Mg 2+ transporter (PDB code 2bbj ) was determined using diffraction data in the resolutio... range 20.0–3.90 Å with 27 320 unique reflections and the model contained 13 805 non-H protein atoms (Lunin et al. , 2006 ▶ ).

Possibly owing to the limited data-to-parameter ratio, three systems (PDB codes 2aeq , 2iny and 2v1c ) have a constant B factor for all atoms and one system (PDB code 2bbj ) has an almost constant B factor for all atoms.

Table 1 Comparison of R cryst and R free factors and thermal parameters for the original models, normal-mode refined models and subsequent multi-group TLS refinement for all structures PDB code 2a0l 2bbj 2pm9 1suq 2vv5 2aeq 2iny 2v1c Original R cryst / R free (%) 34.9/37.9 34.8/39.5 23.9/28.7 26.0/31.6 29.3/31.2 28.5/29.1 34.4/43.3 43.1/45.7 NMRef R cryst / R free (No.

of parameters) (%) 35.1/38.2 (2260) 29.3/34.6 (1500) 21.1/24.3 (600) 25.5/29.9 (200) 25.8/26.8 (420) 23.0/27.0 (900) 32.3/40.8 (200) 29.1/37.9 (600) Table 2 Comparison of residue distributions in the Ramachandran plot for the original models, normal-mode refined models and subsequent multi-group TLS refinement for all structures PDB code Model Ramachandram favored (%) Ramachandran outliers (%) 2a0l Original 77.27 4.66   NMRef 84.50 3.03 2bbj Original 90.00 2.30   NMRef 87.09 2.79 2pm9 Original 74.70 8.38   NMRef 83.69 6.25   NMRef + TLS 83.84 5.95 1suq Original 78.87 4.31   NMRef 85.54 2.77 2vv5 Original 92.38 2.75   NMRef 93.84 2.35   NMRef + TLS 94.01 2.35 2aeq Original 85.95 3.64   NMRef 88.43 2.64   NMRef + TLS 89.92 1.82 2iny Original 59.21 14.48   NMRef 65.50 8.87 2v1c Original 90.79 2.26   NMRef 77.06 5.33

The first two systems (PDB codes 2a0l and 2bbj ) have very large average B factors, indicating a high overall structural flexibility.

Figure 2 ( a ) B -factor profiles for all C α atoms in the original structure of CorA Mg 2+ transporter (PDB code 2bbj ; light line) and the normal-mode refined structure (dark line).

Publication Year: 2009


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4443539

Table 2 RPD2 partial domains corresponding to CATH structural domains Family Pfam CATH CATH length Accession (Pfam) length class (1st to 3rd quartile) UniProt/PDB PF00079 372 3.30.497.10 109 (54 ... 3;172) Q7TP87/1YXA |A PF00118 485 3.50.7.10 177 (181–181) F0YNJ0/1A6D |B 3.30.260.10 47 (38–56) 1.10.560.10 125 (115–134) PF00285 356 1.10.230.10 109 (104–115) Q98FC2/2H12 |A PF00316 325 3.30.540.10 179 (191–192) P00637/1BK4 |A 3.40.190.80 132 (132–135) PF00476 383 1.20.1060.10 126 (115-182) A2WDN6/1KFS |A PF00710 313 3.40.50.1170 214 (214–216) C7ZQZ8/1HFJ |A PF01544 292 3.30.460.20 149 (147–151) D2C657/2BBJ |A 1.20.58.340 76 (76–76) a 1.20.58.340 118 (118–118) PF01571 211 3.30.70.1400 88 (87–88) Q83E96/1NRK |A PF03441 277 1.25.40.80 90 (85–88) Q4V935/1TEZ |A PF03598 412 3.30.1650.10 173 (155–178) B8FZT4/3GIT |A 3.40.970.20 133 (129–146) 3.40.1470.10 93 (89–98) PF03917 370 3.30.1490.80 28 (12–45) Q1RL06/2HGS |A 3.30.470.20 166 (135–193) 1.10.1080.10 41 (33–47) a The CATH:1.20.58.340 domain is annotated to two adjacent locations covered by PF01544 in [PDB:2BBJ |A].

Publication Year: 2015