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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A FUNCTIONALLY UNKNOWN CONSERVED PROTEIN FROM HAEMOPHILUS INFLUENZAE RD KW20
 
Authors :  K. Tan, H. Li, M. Bargassa, S. Clancy, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  06 Jan 10  (Deposition) - 19 Jan 10  (Release) - 19 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,X
Keywords :  Apc85784. 2, Conserved Protein, Haemophilus Influenzae Rd Kw20, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Cbs Domain, Cell Membrane, Membrane, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, H. Li, M. Bargassa, S. Clancy, A. Joachimiak
The Crystal Structure Of A Functionally Unknown Conserved Protein From Haemophilus Influenzae Rd Kw20
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UPF0053 PROTEIN HI0107
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 343-420
    Gene: HI0107
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Strain: RD KW20
 
Molecule 2 - UNKNOWN PEPTIDE FRAGMENT
    Chains: X
    Engineered: YES
    Other Details: PEPTIDE FRAGMENT OF UNKNOWN SOURCE, ITS SEQUENCE HAS BEEN ASSIGNED ACCORDING TO ELECTRON DENSITY
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AX

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MSE3Mod. Amino AcidSELENOMETHIONINE
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:15 , ARG A:17 , ARG A:33 , HOH A:89 , HOH A:142 , HOH A:143 , HOH A:149BINDING SITE FOR RESIDUE PO4 A 79
2AC2SOFTWARESER A:13 , GLU A:30 , ASP A:31 , MSE A:69 , HOH A:151BINDING SITE FOR RESIDUE EDO A 80
3AC3SOFTWAREGLY A:66 , ASP A:67 , HOH A:109BINDING SITE FOR RESIDUE EDO A 81
4AC4SOFTWAREILE A:9 , GLN A:72 , LEU A:78 , HOH A:92 , HOH A:127BINDING SITE FOR RESIDUE EDO A 82

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LAE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LAE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LAE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LAE)

(-) Exons   (0, 0)

(no "Exon" information available for 3LAE)

(-) Sequences/Alignments

Asymmetric/Biological 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:81
 aligned with Y107_HAEIN | Q57017 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:88
                                   342       352       362       372       382       392       402       412        
           Y107_HAEIN   333 STAPSIDKEVIQQSDGSMIIDGSANLRDLNKMFNWELDTEDARTFNGLILEHLEEIPDEGTICEIDGLLITILEVGDNMIKQAKVVKL 420
               SCOP domains d3l       aea_ A: Hypothetical protein HI0107                                            SCOP domains
               CATH domains 3la       eA00 A:-2-78  [code=3.30.465.10, no name defined]                              CATH domains
               Pfam domains ----------CorC_HlyC-3laeA01 A:1-78                                                       Pfam domains
         Sec.struct. author ..e-------ee.....eeee...hhhhhhhhhh.........hhhhhhhhhh........eeee..eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 3lae A  -2 SNA-------IQQSDGSmIIDGSANLRDLNKmFNWELDTEDARTFNGLILEHLEEIPDEGTICEIDGLLITILEVGDNmIKQAKVVKL  78
                              |      -|      |10        20 |      30        40        50        60        70        
                              0       1      8-MSE        22-MSE                                         69-MSE     


Chain X from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 3lae X   1 IFG   3
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CorC_HlyC] (12)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Y107_HAEIN | Q57017)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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(-) Related Entries Specified in the PDB File

2o1r THE NEW DEPOSIT IS TO REPLACE 2O1R RELATED ID: APC85784.2 RELATED DB: TARGETDB