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(-) Description

Title :  CRYSTAL STRUCTURE OF L. MONOCYTOGENES PHOSPHODIESTERASE PGPH HD DOMAIN
 
Authors :  S. Luo, L. Tong
Date :  12 Jan 15  (Deposition) - 11 Feb 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  D  (1x)
Biol. Unit 3:  A (1x),D (1x)
Keywords :  C-Di-Amp, Listeria Monocytogenes, Phosphodiesterase, Hd Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. N. Huynh, S. Luo, D. Pensinger, J. D. Sauer, L. Tong, J. J. Woodward
An Hd-Domain Phosphodiesterase Mediates Cooperative Hydrolysis Of C-Di-Amp To Affect Bacterial Growth And Virulence.
Proc. Natl. Acad. Sci. Usa V. 112 E747 2015
PubMed-ID: 25583510  |  Reference-DOI: 10.1073/PNAS.1416485112

(-) Compounds

Molecule 1 - LMO1466 PROTEIN
    Chains: D, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LMO1466, PGPH
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 169963
    Strain: ATCC BAA-679 / EGD-E

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AD
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  D
Biological Unit 3 (1x): A (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1FE4Ligand/IonFE (III) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP D:544 , HIS D:580 , HIS D:604 , HIS D:605 , FE D:802 , HOH D:965BINDING SITE FOR RESIDUE FE D 801
2AC2SOFTWAREHIS D:514 , HIS D:543 , ASP D:544 , ASP D:648 , FE D:801 , HOH D:965BINDING SITE FOR RESIDUE FE D 802
3AC3SOFTWAREHIS A:514 , HIS A:543 , ASP A:544 , ASP A:648 , FE A:802 , HOH A:955BINDING SITE FOR RESIDUE FE A 801
4AC4SOFTWAREASP A:544 , HIS A:580 , HIS A:604 , HIS A:605 , FE A:801 , HOH A:955BINDING SITE FOR RESIDUE FE A 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S1C)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly D:633 -Pro D:634
2Thr D:658 -Glu D:659
3Gly A:633 -Pro A:634
4Thr A:658 -Glu A:659

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S1C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S1C)

(-) Exons   (0, 0)

(no "Exon" information available for 4S1C)

(-) 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:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhh.....hhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s1c A 497 NHPLLKKILMKAPGTYHHSMMVANLAEACADKIGANSLLVRVGCFYHDIGKTLRPPYFVENQLQGINPHDRLTPEQSRDIILSHTKDGAEILKENHMPQPIIDIALQHHGTTLLKYFYFKAKEVKEADYRYSGPKPQTKEIAIINISDSVEAAVRSSTEPTMAKITEIIDGIIKDRFLDGQFTECDITIQEIKIIRDTLIATLNGIYH 708
                                   506       516       526       536       546       556       566       576       586       596       606       616  ||   630       640       650       660       670       680       690       700        
                                                                                                                                                    619|                                                                                    
                                                                                                                                                     624                                                                                    


Chain D from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhh.....hhhhhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s1c D 497 NHPLLKKILMKAPGTYHHSMMVANLAEACADKIGANSLLVRVGCFYHDIGKTLRPPYFVENQLQGINPHDRLTPEQSRDIILSHTKDGAEILKENHMPQPIIDIALQHHGTTLLKYFYFKAKDVKEADYRYSGPKPQTKEIAIINISDSVEAAVRSSTEPTMAKITEIIDGIIKDRFLDGQFTECDITIQEIKIIRDTLIATLNGIYH 708
                                   506       516       526       536       546       556       566       576       586       596       606       616 ||    630       640       650       660       670       680       690       700        
                                                                                                                                                   618|                                                                                     
                                                                                                                                                    623
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4S1C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S1C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S1C)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        PGPH_LISM4 | A0A0H3GGY3: 4s1b
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(-) Related Entries Specified in the PDB File

4s1b