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(-) Description

Title :  CRYSTAL STRUCTURE OF L-LACTATE DEHYDROGENASE FROM BACILLUS CEREUS ATCC 14579, NYSGRC TARGET 029452
 
Authors :  V. N. Malashkevich, J. B. Bonanno, R. Bhosle, R. Toro, B. Hillerich, A. G S. Garforth, A. Kar, M. K. Chan, J. Lafluer, H. Patel, B. Matikainen, S. S. Lim, A. Celikgil, G. Villegas, B. Evans, J. Love, A. Fiser, K. Khafiz R. Seidel, S. C. Almo, New York Structural Genomics Research Con (Nysgrc)
Date :  10 Jul 13  (Deposition) - 31 Jul 13  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Structural Genomics, Protein Structure Initiative, Nysgrc, Psi- Biology, New York Structural Genomics Research Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, J. B. Bonanno, R. Bhosle, R. Toro, B. Hillerich, A. Gizzi, S. Garforth, A. Kar, M. K. Chan, J. Lafluer, H. Patel, B. Matikainen, S. Chamala, S. Lim, A. Celikgil, G. Villegas, B. Evans, J. Love, A. Fiser, K. Khafizov, R. Seidel, S. C. Almo
Crystal Structure Of L-Lactate Dehydrogenase From Bacillus Cereus Atcc 14579, Nysgrc Target 029452
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L-LACTATE DEHYDROGENASE 1
    Chains: A, B
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BC_1924, LDH, LDH1
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 226900
    Strain: ATCC 14579
    Synonym: L-LDH 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4LMR)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LMR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:123 -Pro A:124
2Asn B:123 -Pro B:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LMR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LMR)

(-) Exons   (0, 0)

(no "Exon" information available for 4LMR)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4lmra1 A:3-147 automated matches                                                                                                                d4lmra2 A:148-314 automated matches                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lmr A   3 KGINRVVLVGTGAVGCSYAYCmINQAVAEEFVLVDVNEAKAEGEAmDLSHAVPFAPAPTRVWKGSYEDCKDADLVVITAGLPQKPGETRLDLVEKNAKIFKQIVRSImDSGFDGIFLIATNPVDILTYVTWKESGLPKERVIGSGTTLDSARFRYmLGEYFDIGPHNIHAYIIGEHGDTELPVWSHVSVGIQKLQTLLEKDNTYNQEDLDKIFINVRDAAYHIIERKGATYYGIGmSLLRVTKAILNDENSVLTVSAYLEGQYGQKDVYIGVPAVLNRGGVREILEVELSEDEELKFDHSVQVLKETmAPVL 314
                                    12        22 |      32        42     |  52        62        72        82        92       102       112       122       132       142       152     | 162       172       182       192       202       212       222       232     | 242       252       262       272       282       292       302       312  
                                                24-MSE                  48-MSE                                                       110-MSE                                         158-MSE                                                                         238-MSE                                                                 310-MSE


Chain B from PDB  Type:PROTEIN  Length:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4lmrb1 B:3-147 automated matches                                                                                                                d4lmrb2 B:148-314 automated matches                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lmr B   3 KGINRVVLVGTGAVGCSYAYCmINQAVAEEFVLVDVNEAKAEGEAmDLSHAVPFAPAPTRVWKGSYEDCKDADLVVITAGLPQKPGETRLDLVEKNAKIFKQIVRSImDSGFDGIFLIATNPVDILTYVTWKESGLPKERVIGSGTTLDSARFRYmLGEYFDIGPHNIHAYIIGEHGDTELPVWSHVSVGIQKLQTLLEKDNTYNQEDLDKIFINVRDAAYHIIERKGATYYGIGmSLLRVTKAILNDENSVLTVSAYLEGQYGQKDVYIGVPAVLNRGGVREILEVELSEDEELKFDHSVQVLKETmAPVL 314
                                    12        22 |      32        42     |  52        62        72        82        92       102       112       122       132       142       152     | 162       172       182       192       202       212       222       232     | 242       252       262       272       282       292       302       312  
                                                24-MSE                  48-MSE                                                       110-MSE                                         158-MSE                                                                         238-MSE                                                                 310-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LMR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LMR)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:123 - Pro A:124   [ RasMol ]  
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 Related Entries

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        LDH1_BACCR | Q81EP4: 4ln1

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