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Structure of apo- and monometalated forms of NDM-1--a highly potent carbapenem-hydrolyzing metallo-?-lactamase.

(2011) PLoS One 6

PubMed: 21931780 | PubMedCentral: PMC3169612 | DOI: 10.1371/journal.pone.0024621

Data collection statistics NDM-1 Δ38 (39–270) NDM-1 Δ36NY (37–270) NDM-1 Δ36NY (37–270) mZnNDM-1 Δ36NY(37–270) Space group P2 1 P2 1 I22... P4 3 2 1 2 Unit cell (Å) a  = 59.71 b  = 51.11 c  = 70.68 β  = 106.96 a  = 59.76 b  = 50.86 c  = 70.72 β  = 106.98 a  = 66.05 b  = 83.27 c  = 10.5.4 a  = 97.94 b  = 97.94 c  = 187.55 Wavelength (Å) 0.9793 0.9793 0.9792 1.2825 Highest Resolution bin (Å) 2.03-2.00 2.39-2.35 2.34-2.30 2.31-2.27 Number of observed reflections 26835 (1377) b 16892 (709) b 12326(528) b 42642 (2066) b R merge (%) a 15.3 (55.7) b 14.4 (44.8) b 9.1(33.4) b 10.4 (57.0) b Completeness (%) 95.0 (96.8) b 97.6 (80.9) b 95.5(84.3) b 99.1 (98.1) b I /σ I 6.3 (2.5) b 5.9 (2.1) b 11.9(3.5) b 6.3 (2.0) b Phasing and Refinement MR MR MR MR Search model Chain A of 2YZ3 Chain A of 3RKJ Chain A of 3RKJ Chain A of 3Q6X Phasing resolution range (Å) 38.4-2.00 40.7-2.35 36.9-2.31 38.4-2.27 Refinement resolution range (Å) 38.4-2.00 40.7-2.35 36.9-2.31 38.4-2.27 R cryst (%) 19.2 20.8 20.3 18.3 R free (%) 24.3 28.3 26.0 23.6 Number of protein residues 464 464 237 928 Solvent molecules 262 170 61 324 Bond lengths (Å) 0.007 0.017 0.012 0.011 Bond angles (deg) 1.19 1.61 1.52 1.33 B-factors (Å 2 ) 30.1 30.6 50.6 32.6 Protein main chain 25.83 28.62 46.60 30.08 Protein side chain 31.04 30.31 52.92 33.51 Solvent (Water) 38.49 34.58 47.28 37.46 Wilson B-factor (Å 2 ) 25.89 24.97 36.45 30.32 Ramachandran Plot (%) c Preferred 97.4 98.0 97.8 99.5 Generously allowed 2.6 2.0 2.2 0.4 Disallowed 0 0 0 0.1 PDB ID 3RKJ 3RKK 3SBL 3SFP a R merge  =  , where Ii is the intensity for the i th measurement of an equivalent reflection with indices h , k , and l .

A. Structures of six NDM-1 molecules (identified using PDB ids) were aligned (PDB id 3RKJ (this work) molecule A - blue, PDB id 3RKJ (this work) molecule B - light blue, PDB id 3SBL (this work) molecule A - green, PDB id 3RKK (this work) molecule B – red, PDB id 3SFP (this work) molecule B – violet and PDB id 3Q6X [49] molecule B – wheat), hAmp is a hydrolyzed ampicillin and Zn1′ and Zn2′ are zinc atoms from the structure of NDM-1 (PDB id 3Q6X molecule B) and Zn1″ is from the structure of monozinc NDM-1.

PDB accession code The atomic coordinates and structure factors have been deposited in the PDB with accession code 3RKJ, 3RKK, 3SBL and 3SFP.

Publication Year: 2011