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Crystallographic R (crystallographic + r)

Distribution by Scientific Domains
Chemistry100%

Terms modified by Crystallographic R

  • crystallographic r factor
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    Selected Abstracts

    Crystal structure of archaeal highly thermostable L -aspartate dehydrogenase/NAD/citrate ternary complex

    FEBS JOURNAL, Issue 16 2007
    Kazunari Yoneda
    The crystal structure of the highly thermostable l -aspartate dehydrogenase (l -aspDH; EC 1.4.1.21) from the hyperthermophilic archaeon Archaeoglobus fulgidus was determined in the presence of NAD and a substrate analog, citrate. The dimeric structure of A. fulgidusl -aspDH was refined at a resolution of 1.9 Å with a crystallographic R -factor of 21.7% (Rfree = 22.6%). The structure indicates that each subunit consists of two domains separated by a deep cleft containing an active site. Structural comparison of the A. fulgidusl -aspDH/NAD/citrate ternary complex and the Thermotoga maritimal -aspDH/NAD binary complex showed that A. fulgidusl -aspDH assumes a closed conformation and that a large movement of the two loops takes place during substrate binding. Like T. maritimal -aspDH, the A. fulgidus enzyme is highly thermostable. But whereas a large number of inter- and intrasubunit ion pairs are responsible for the stability of A. fulgidusl -aspDH, a large number of inter- and intrasubunit aromatic pairs stabilize the T. maritima enzyme. Thus stabilization of these two l -aspDHs appears to be achieved in different ways. This is the first detailed description of substrate and coenzyme binding to l -aspDH and of the molecular basis of the high thermostability of a hyperthermophilic l -aspDH. [source]

    Structural features of a zinc binding site in the superantigen strepococcal pyrogenic exotoxin A (SpeA1): Implications for MHC class II recognition

    PROTEIN SCIENCE, Issue 6 2001
    Matthew Baker
    Abstract Streptococcal pyrogenic exotoxin A (SpeA) is produced by Streptococcus pyogenes, and has been associated with severe infections such as scarlet fever and Streptococcal Toxic Shock Syndrome (STSS). In this study, the crystal structure of SpeA1 (the product of speA allele 1) in the presence of 2.5 mM zinc was determined at 2.8 Å resolution. The protein crystallizes in the orthorhombic space group P21212, with four molecules in the crystallographic asymmetric unit. The final structure has a crystallographic R -factor of 21.4% for 7,031 protein atoms, 143 water molecules, and 4 zinc atoms (one zinc atom per molecule). Four protein ligands,Glu 33, Asp 77, His 106, and His 110,form a zinc binding site that is similar to the one observed in a related superantigen, staphylococcoal enterotoxin C2. Mutant toxin forms substituting Ala for each of the zinc binding residues were generated. The affinity of these mutants for zinc ion confirms the composition of this metal binding site. The implications of zinc binding to SpeA1 for MHC class II recognition are explored using a molecular modeling approach. The results indicate that, despite their common overall architecture, superantigens appear to have multiple ways of complex formation with MHC class II molecules. [source]

    Structure of the transcription regulator CcpA from Lactococcus lactis

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2007
    Bernhard Loll
    Catabolite control protein A (CcpA) functions as master transcriptional regulator of carbon catabolism in Firmicutes. It belongs to the family of bacterial repressor/regulator proteins. Here, the crystal structure of the 76,kDa homodimeric CcpA protein from Lactococcus lactis subsp. lactis IL1403 is presented at 1.9,Å resolution in the absence of cognate DNA. The phases were derived by molecular replacement and the structure was refined to crystallographic R and Rfree factors of 0.177 and 0.211, respectively. The presence of a sulfate molecule in the direct vicinity of a putative effector-binding site in the monomer allowed the derivation of a model for the possible binding of small organic effector molecules. [source]

    Structure of the isoaspartyl peptidase with l -­asparaginase activity from Escherichia coli

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2004
    Adam Prahl
    The crystal structure of the Escherichia coli enzyme (EcAIII) with isoaspartyl dipeptidase and l -asparaginase activity has been solved and refined to a resolution of 1.65,Å, with crystallographic R -factor and Rfree values of 0.178 and 0.209, respectively. EcAIII belongs to the family of N-terminal hydrolases. The amino-acid sequence of EcAIII is homologous to those of putative asparaginases from plants. The structure of EcAIII is similar to the structures of glycosylasparaginases. The mature and catalytically active form of EcAIII is a heterotetramer consisting of two ,-subunits and two ,-subunits. Both of the equivalent active sites present in the EcAIII tetramer is assisted by a metal-binding site. The metal cations, modelled here as Na+, have not previously been observed in glycosylasparaginases. This reported structure helps to explain the inability of EcAIII and other plant-type asparaginases to hydrolyze N4 -(,- N -acetylglucosaminyl)- l -asparagine, the substrate of glycosylasparaginases. [source]