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(-) Description

Title :  CRYSTAL STRUCTURE OF DPS PROTEIN FROM VIBRIO CHOLERAE O1, A MEMBER OF A BROAD SUPERFAMILY OF FERRITIN-LIKE DIIRON-CARBOXYLATE PROTEINS
 
Authors :  B. Nocek, S. Peterson, M. Gu, Z. Otwinowski, W. Anderson, A. Joachimiak
Date :  18 Aug 09  (Deposition) - 08 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Csgid, Dps Family Protein, Sad, Niaid, Metal Transport, Structural Genomics, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, S. Peterson, M. Gu, Z. Otwinowski, W. Anderson, A. Joachimia
Crystal Structure Of Dps Protein From Vibrio Cholerae O1, A Member Of A Broad Superfamily Of Ferritin-Like Diiron-Carboxylate Proteins
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DPS FAMILY PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VC_0139
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid: 243277
    Strain: N16961

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 28)

Asymmetric Unit (2, 28)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 72)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE72Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:77 , HIS A:80 , SER A:81BINDING SITE FOR RESIDUE CL A 1001
2AC2SOFTWAREARG B:77 , MSE B:79 , HIS B:80 , SER B:81BINDING SITE FOR RESIDUE CL B 1001
3AC3SOFTWAREARG C:77 , HIS C:80 , SER C:81 , HOH C:571BINDING SITE FOR RESIDUE CL C 1001
4AC4SOFTWAREARG D:77 , HIS D:80 , SER D:81BINDING SITE FOR RESIDUE CL D 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IQ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IQ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IQ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IQ1)

(-) Exons   (0, 0)

(no "Exon" information available for 3IQ1)

(-) 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:156
 aligned with Q9KVK4_VIBCH | Q9KVK4 from UniProtKB/TrEMBL  Length:156

    Alignment length:156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      
         Q9KVK4_VIBCH     1 MATNLIGLDTTQSQKLANALNNLLANYQVFYMNTRGYHWNIQGKEFFELHAKFEEIYTDLQLKIDELAERILTLSARPMHSFSGYLKAAQIKEHTDSIDGRSSMQGLVDGFSILLHQQRDILELAGETGDEGTSALMSDYIREQEKLVWMLNAWLK 156
               SCOP domains d3iq1a_ A: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3iq1 A   1 mATNLIGLDTTQSQKLANALNNLLANYQVFYmNTRGYHWNIQGKEFFELHAKFEEIYTDLQLKIDELAERILTLSARPmHSFSGYLKAAQIKEHTDSIDGRSSmQGLVDGFSILLHQQRDILELAGETGDEGTSALmSDYIREQEKLVWmLNAWLK 156
                            |       10        20        30 |      40        50        60        70        80        90       100   |   110       120       130      |140       150      
                            |                             32-MSE                                         79-MSE                  104-MSE                          137-MSE      150-MSE  
                            1-MSE                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:159
 aligned with Q9KVK4_VIBCH | Q9KVK4 from UniProtKB/TrEMBL  Length:156

    Alignment length:159
                               1                                                                                                                                                           
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147         
         Q9KVK4_VIBCH     - ---MATNLIGLDTTQSQKLANALNNLLANYQVFYMNTRGYHWNIQGKEFFELHAKFEEIYTDLQLKIDELAERILTLSARPMHSFSGYLKAAQIKEHTDSIDGRSSMQGLVDGFSILLHQQRDILELAGETGDEGTSALMSDYIREQEKLVWMLNAWLK 156
               SCOP domains d3iq1b_ B: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iq1 B  -2 SNAmATNLIGLDTTQSQKLANALNNLLANYQVFYmNTRGYHWNIQGKEFFELHAKFEEIYTDLQLKIDELAERILTLSARPmHSFSGYLKAAQIKEHTDSIDGRSSmQGLVDGFSILLHQQRDILELAGETGDEGTSALmSDYIREQEKLVWmLNAWLK 156
                               |     7        17        27    |   37        47        57        67        77 |      87        97      |107       117       127       137       147  |      
                               1-MSE                         32-MSE                                         79-MSE                  104-MSE                          137-MSE      150-MSE  


Chain C from PDB  Type:PROTEIN  Length:157
 aligned with Q9KVK4_VIBCH | Q9KVK4 from UniProtKB/TrEMBL  Length:156

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
         Q9KVK4_VIBCH     - -MATNLIGLDTTQSQKLANALNNLLANYQVFYMNTRGYHWNIQGKEFFELHAKFEEIYTDLQLKIDELAERILTLSARPMHSFSGYLKAAQIKEHTDSIDGRSSMQGLVDGFSILLHQQRDILELAGETGDEGTSALMSDYIREQEKLVWMLNAWLK 156
               SCOP domains d3iq1c_ C: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iq1 C   0 AmATNLIGLDTTQSQKLANALNNLLANYQVFYmNTRGYHWNIQGKEFFELHAKFEEIYTDLQLKIDELAERILTLSARPmHSFSGYLKAAQIKEHTDSIDGRSSmQGLVDGFSILLHQQRDILELAGETGDEGTSALmSDYIREQEKLVWmLNAWLK 156
                             |       9        19        29  |     39        49        59        69        79        89        99    |  109       119       129       139       149|      
                             1-MSE                         32-MSE                                         79-MSE                  104-MSE                          137-MSE      150-MSE  


Chain D from PDB  Type:PROTEIN  Length:159
 aligned with Q9KVK4_VIBCH | Q9KVK4 from UniProtKB/TrEMBL  Length:156

    Alignment length:159
                               1                                                                                                                                                           
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147         
         Q9KVK4_VIBCH     - ---MATNLIGLDTTQSQKLANALNNLLANYQVFYMNTRGYHWNIQGKEFFELHAKFEEIYTDLQLKIDELAERILTLSARPMHSFSGYLKAAQIKEHTDSIDGRSSMQGLVDGFSILLHQQRDILELAGETGDEGTSALMSDYIREQEKLVWMLNAWLK 156
               SCOP domains d3iq1d_ D: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iq1 D  -2 SNAmATNLIGLDTTQSQKLANALNNLLANYQVFYmNTRGYHWNIQGKEFFELHAKFEEIYTDLQLKIDELAERILTLSARPmHSFSGYLKAAQIKEHTDSIDGRSSmQGLVDGFSILLHQQRDILELAGETGDEGTSALmSDYIREQEKLVWmLNAWLK 156
                               |     7        17        27    |   37        47        57        67        77 |      87        97      |107       117       127       137       147  |      
                               1-MSE                         32-MSE                                         79-MSE                  104-MSE                          137-MSE      150-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  (1, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IQ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IQ1)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9KVK4_VIBCH | Q9KVK4)
molecular function
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0016722    oxidoreductase activity, oxidizing metal ions    Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered.
biological process
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    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.
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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(-) Related Entries Specified in the PDB File

1jig CRYSTAL STRUCTURE OF DLP-2 FROM BACILLUS ANTHRACIS RELATED ID: IDP01318 RELATED DB: TARGETDB