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(-) Description

Title :  THE X-RAY STRUCTURE OF THE CYANOBACTERIA SYNECHOCYSTIS HEMOGLOBIN "CYANOGLOBIN" WITH CYANIDE LIGAND
 
Authors :  J. T. Trent Iii, S. Kundu, J. A. Hoy, M. S. Hargrove
Date :  22 Jan 04  (Deposition) - 21 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym./Biol. Unit :  A
Keywords :  2 On 2 Helical Fold, Globin, Heme, Iron, Hemoglobin, Cyanobacteria, Oxygen Binding, Hexacoordinate, Truncated, Oxygen Storage-Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. T. Trent Iii, S. Kundu, J. A. Hoy, M. S. Hargrove
Crystallographic Analysis Of Synechocystis Cyanoglobin Reveals The Structural Changes Accompanying Ligand Binding In A Hexacoordinate Hemoglobin.
J. Mol. Biol. V. 341 1097 2004
PubMed-ID: 15289104  |  Reference-DOI: 10.1016/J.JMB.2004.05.070

(-) Compounds

Molecule 1 - CYANOGLOBIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GLBN, SLR2097
    Organism Scientific: SYNECHOCYSTIS SP.
    Organism Taxid: 1148
    Strain: PCC 6803
    Synonym: HEMOGLOBIN, HB

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CYN1Ligand/IonCYANIDE ION
2FLC1Ligand/IonCITRATE ANION
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:50 , TYR A:53 , TYR A:65 , MET A:66 , HIS A:77 , ALA A:116 , HIS A:117 , ASP A:120 , HOH A:247 , HOH A:280 , HOH A:282 , HOH A:306 , HOH A:321 , HOH A:339 , HOH A:360 , HOH A:375BINDING SITE FOR RESIDUE FLC A 227
2AC2SOFTWARETYR A:22 , GLN A:43 , GLN A:47 , HEM A:125BINDING SITE FOR RESIDUE CYN A 126
3AC3SOFTWAREILE A:31 , PHE A:34 , PHE A:35 , VAL A:38 , GLN A:43 , HIS A:46 , GLN A:47 , PHE A:50 , TYR A:61 , GLY A:63 , ARG A:64 , MET A:66 , HIS A:70 , LEU A:73 , LEU A:79 , PHE A:84 , VAL A:87 , HIS A:117 , CYN A:126 , HOH A:302 , HOH A:322 , HOH A:365BINDING SITE FOR RESIDUE HEM A 125

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S69)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S69)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S69)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBIN_FAM_2PS01213 Protozoan/cyanobacterial globins signature.TRHBN_SYNY350-70  1A:50-70

(-) Exons   (0, 0)

(no "Exon" information available for 1S69)

(-) 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:123
 aligned with TRHBN_SYNY3 | P73925 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:123
                                    11        21        31        41        51        61        71        81        91       101       111       121   
          TRHBN_SYNY3     2 STLYEKLGGTTAVDLAVDKFYERVLQDDRIKHFFADVDMAKQRAHQKAFLTYAFGGTDKYDGRYMREAHKELVENHGLNGEHFDAVAEDLLATLKEMGVPEDLIAEVAAVAGAPAHKRDVLNQ 124
               SCOP domains d1s69a_ A: Protozoan/bacterial hemoglobin                                                                                   SCOP domains
               CATH domains 1s69A00 A:2-124 Globins                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------GLOBIN_FAM_2         ------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s69 A   2 STLYEKLGGTTAVDLAVDKFYERVLQDDRIKHFFADVDMAKQRAHQKAFLTYAFGGTDKYDGRYMREAHKELVENHGLNGEHFDAVAEDLLATLKEMGVPEDLIAEVAAVAGAPAHKRDVLNQ 124
                                    11        21        31        41        51        61        71        81        91       101       111       121
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  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: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1S69)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRHBN_SYNY3 | P73925)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0005344    oxygen transporter activity    Enables the directed movement of oxygen into, out of or within a cell, or between cells.
biological process
    GO:0015671    oxygen transport    The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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  1s69
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  TRHBN_SYNY3 | P73925
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRHBN_SYNY3 | P73925: 1mwb 1rtx 1s6a 2hz1 2hz2 2hz3

(-) Related Entries Specified in the PDB File

1s6a