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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE BACTERIOFERRITIN FROM CAMPYLOBACTER JEJUNI
 
Authors :  Y. Kim, M. Gu, L. Papazisi, W. Anderson, A. Joachimiak
Date :  01 Dec 09  (Deposition) - 19 Jan 10  (Release) - 19 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Alpha-Helix, Bacterial Ferritin Fold, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Cytoplasm, Iron, Iron Storage, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, M. Gu, L. Papazisi, W. Anderson, A. Joachimiak
Crystal Structure Of Putative Bacterioferritin From Campylobacter Jejuni
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE BACTERIOFERRITIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MAGIC
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PMCSG7
    Expression System Vector Type: PLASMID
    Organism Scientific: CAMPYLOBACTER JEJUNI
    Organism Taxid: 192222
    Strain: NCTC 11168

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 75)

Asymmetric Unit (5, 75)
No.NameCountTypeFull Name
1ACY24Ligand/IonACETIC ACID
2BU13Ligand/Ion1,4-BUTANEDIOL
3GOL2Ligand/IonGLYCEROL
4MSE20Mod. Amino AcidSELENOMETHIONINE
5ZN26Ligand/IonZINC ION
Biological Unit 1 (4, 147)
No.NameCountTypeFull Name
1ACY72Ligand/IonACETIC ACID
2BU19Ligand/Ion1,4-BUTANEDIOL
3GOL6Ligand/IonGLYCEROL
4MSE60Mod. Amino AcidSELENOMETHIONINE
5ZN-1Ligand/IonZINC ION

(-) Sites  (55, 55)

Asymmetric Unit (55, 55)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:90 , GLU A:93 , ACY A:159 , ZN A:164 , HOH A:363 , GLU D:93BINDING SITE FOR RESIDUE ACY A 151
02AC2SOFTWAREMSE A:73 , ACY A:154 , GLN C:69 , ZN C:165BINDING SITE FOR RESIDUE ACY A 150
03AC3SOFTWAREGLU A:38 , GLU A:41 , GLU A:45 , ACY A:153 , ZN A:163BINDING SITE FOR RESIDUE ACY A 152
04AC4SOFTWAREGLU A:38 , GLU A:41 , ACY A:152 , ZN A:162 , ACY B:154BINDING SITE FOR RESIDUE ACY A 153
05AC5SOFTWAREHIS A:16 , VAL A:19 , ACY A:150 , HOH A:201 , THR C:67 , CYS C:68 , GLN C:69 , ACY C:152 , ZN C:165BINDING SITE FOR RESIDUE ACY A 154
06AC6SOFTWARETHR A:67 , CYS A:68 , GLN A:69 , ZN A:165 , HOH A:291 , HIS C:16 , LYS C:20BINDING SITE FOR RESIDUE ACY A 155
07AC7SOFTWAREASP A:84 , HOH A:274 , HOH A:541 , CYS B:147 , ZN B:167 , LYS C:64BINDING SITE FOR RESIDUE ACY A 157
08AC8SOFTWARETHR A:142 , PHE C:34 , HOH C:547BINDING SITE FOR RESIDUE ACY A 158
09AC9SOFTWARELEU A:89 , GLU A:93 , ACY A:151 , ZN A:164 , GLU D:93BINDING SITE FOR RESIDUE ACY A 159
10BC1SOFTWARELEU A:31 , PHE A:33 , PHE A:34 , HOH A:186 , THR B:142 , BU1 B:155 , HOH B:181BINDING SITE FOR RESIDUE GOL A 160
11BC2SOFTWAREHIS A:37 , ZN A:162 , HOH A:371 , MSE B:138 , ACY B:154 , HOH B:198 , ZN C:164BINDING SITE FOR RESIDUE ZN A 161
12BC3SOFTWAREGLU A:38 , GLU A:41 , ACY A:153 , ZN A:161 , ACY B:154BINDING SITE FOR RESIDUE ZN A 162
13BC4SOFTWAREGLU A:45 , ACY A:152 , HOH A:207 , HOH A:447BINDING SITE FOR RESIDUE ZN A 163
14BC5SOFTWAREASP A:52 , GLU A:56 , HOH A:444 , HIS C:25 , TYR C:44 , ZN C:162BINDING SITE FOR RESIDUE ZN A 156
15BC6SOFTWAREGLU A:93 , ACY A:151 , ACY A:159 , GLU D:93BINDING SITE FOR RESIDUE ZN A 164
16BC7SOFTWARECYS A:68 , ACY A:155 , HOH A:189 , HOH A:530BINDING SITE FOR RESIDUE ZN A 165
17BC8SOFTWAREGLU A:111 , GLU D:111 , GLU D:114 , ACY D:151BINDING SITE FOR RESIDUE ZN A 167
18BC9SOFTWARECYS A:147 , HOH A:524 , CYS C:85 , HOH C:525 , HOH C:540BINDING SITE FOR RESIDUE ZN A 168
19CC1SOFTWAREGLU B:38 , GLU B:41 , GLU B:45 , ACY B:153 , ZN B:164BINDING SITE FOR RESIDUE ACY B 151
20CC2SOFTWARETHR B:67 , CYS B:68 , GLN B:69 , ZN B:165 , HOH B:212 , HIS D:16BINDING SITE FOR RESIDUE ACY B 152
21CC3SOFTWAREPHE A:34 , HIS A:37 , GLU A:38 , GLU A:41 , ACY A:153 , ZN A:161 , ZN A:162 , LYS B:134 , MSE B:138 , HOH B:198BINDING SITE FOR RESIDUE ACY B 154
22CC4SOFTWAREGLU B:38 , GLU B:41 , ACY B:151 , ZN B:161BINDING SITE FOR RESIDUE ACY B 153
23CC5SOFTWARELYS B:96 , GLN B:97 , GLU B:100 , HOH B:522 , HOH B:538BINDING SITE FOR RESIDUE GOL B 150
24CC6SOFTWARELEU A:31 , GOL A:160 , SER B:35 , ILE B:36 , TYR B:39 , HOH B:271 , HOH B:317BINDING SITE FOR RESIDUE BU1 B 155
25CC7SOFTWAREGLU B:38 , GLU B:41 , ACY B:153 , ZN B:162 , HOH B:225BINDING SITE FOR RESIDUE ZN B 161
26CC8SOFTWAREHIS B:37 , ZN B:161 , ZN B:163 , HOH B:206 , HOH B:225 , HOH D:402BINDING SITE FOR RESIDUE ZN B 162
27CC9SOFTWAREHIS B:25 , TYR B:44 , ZN B:162 , ASP D:52 , GLU D:56 , HOH D:402BINDING SITE FOR RESIDUE ZN B 163
28DC1SOFTWAREGLU B:45 , ACY B:151 , HOH B:261 , HOH B:476BINDING SITE FOR RESIDUE ZN B 164
29DC2SOFTWARECYS B:68 , ACY B:152 , HOH B:193 , HOH B:527BINDING SITE FOR RESIDUE ZN B 165
30DC3SOFTWARECYS B:85 , HOH B:521 , CYS C:147 , HOH C:520BINDING SITE FOR RESIDUE ZN B 166
31DC4SOFTWARECYS A:85 , ACY A:157 , HOH A:215 , CYS B:147 , HOH B:418BINDING SITE FOR RESIDUE ZN B 167
32DC5SOFTWAREVAL A:81 , ACY A:154 , CYS C:68 , ZN C:165BINDING SITE FOR RESIDUE ACY C 152
33DC6SOFTWAREGLU C:38 , GLU C:41 , ACY C:155 , ACY C:156 , ZN C:161BINDING SITE FOR RESIDUE ACY C 154
34DC7SOFTWARELYS A:134 , HOH A:198 , PHE C:34 , GLU C:38 , GLU C:41 , ACY C:154 , ZN C:161 , ZN C:162BINDING SITE FOR RESIDUE ACY C 155
35DC8SOFTWAREGLU C:38 , GLU C:41 , GLU C:45 , ACY C:154 , ZN C:166BINDING SITE FOR RESIDUE ACY C 156
36DC9SOFTWAREGLU C:38 , GLU C:41 , ACY C:154 , ACY C:155 , ZN C:162BINDING SITE FOR RESIDUE ZN C 161
37EC1SOFTWAREZN A:156 , HOH A:198 , HOH A:444 , HIS C:37 , ACY C:155 , ZN C:161BINDING SITE FOR RESIDUE ZN C 162
38EC2SOFTWAREHIS A:25 , TYR A:44 , ZN A:161 , HOH A:371 , ASP C:52 , GLU C:56BINDING SITE FOR RESIDUE ZN C 164
39EC3SOFTWAREACY A:150 , ACY A:154 , CYS C:68 , ACY C:152BINDING SITE FOR RESIDUE ZN C 165
40EC4SOFTWAREGLU C:45 , ACY C:156 , HOH C:194 , HOH C:453BINDING SITE FOR RESIDUE ZN C 166
41EC5SOFTWAREGLU A:111 , LYS A:115 , ZN A:167 , HOH A:184 , SER B:117 , HOH B:192 , GLU D:111 , GLU D:114BINDING SITE FOR RESIDUE ACY D 151
42EC6SOFTWAREGLU D:38 , GLU D:41 , ACY D:153 , ZN D:163 , HOH D:567BINDING SITE FOR RESIDUE ACY D 152
43EC7SOFTWAREGLU D:38 , GLU D:41 , LYS D:42 , ACY D:152 , ZN D:163 , ZN D:165BINDING SITE FOR RESIDUE ACY D 153
44EC8SOFTWAREGLU B:56 , HIS D:37 , LYS D:134 , TRP D:137 , ZN D:161 , ZN D:162 , HOH D:167 , HOH D:326BINDING SITE FOR RESIDUE ACY D 154
45EC9SOFTWAREHIS B:16 , VAL B:19 , LYS B:20 , HOH B:386 , THR D:67 , CYS D:68 , GLN D:69 , ACY D:156 , ZN D:164BINDING SITE FOR RESIDUE ACY D 155
46FC1SOFTWAREGLN D:69 , ACY D:155 , ZN D:164BINDING SITE FOR RESIDUE ACY D 156
47FC2SOFTWAREALA A:82 , CYS D:147 , ZN D:166 , HOH D:517 , HOH D:559BINDING SITE FOR RESIDUE ACY D 157
48FC3SOFTWARELEU D:31 , GLN D:32 , PHE D:33 , PHE D:34 , THR D:142 , BU1 D:159 , HOH D:234BINDING SITE FOR RESIDUE BU1 D 158
49FC4SOFTWARELEU D:31 , SER D:35 , BU1 D:158 , HOH D:500BINDING SITE FOR RESIDUE BU1 D 159
50FC5SOFTWAREHIS D:37 , ACY D:154 , ZN D:162 , ZN D:163 , HOH D:167 , HOH D:326BINDING SITE FOR RESIDUE ZN D 161
51FC6SOFTWAREASP B:52 , GLU B:56 , HIS D:25 , TYR D:44 , ACY D:154 , ZN D:161 , HOH D:326BINDING SITE FOR RESIDUE ZN D 162
52FC7SOFTWAREGLU D:38 , GLU D:41 , ACY D:152 , ACY D:153 , ZN D:161 , HOH D:167BINDING SITE FOR RESIDUE ZN D 163
53FC8SOFTWARECYS D:68 , ACY D:155 , ACY D:156 , HOH D:531BINDING SITE FOR RESIDUE ZN D 164
54FC9SOFTWAREGLU D:45 , ACY D:153 , HOH D:282BINDING SITE FOR RESIDUE ZN D 165
55GC1SOFTWARECYS D:85 , CYS D:147 , ACY D:157 , HOH D:517 , HOH D:518BINDING SITE FOR RESIDUE ZN D 166

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KWO)

(-) 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:149
 aligned with DPS_CAMJE | Q0P891 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:149
                              1                                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138         
            DPS_CAMJE     - --MSVTKQLLQMQADAHHLWVKFHNYHWNVKGLQFFSIHEYTEKAYEEMAELFDSCAERVLQLGEKAITCQKVLMENAKSPKVAKDCFTPLEVIELIKQDYEYLLAEFKKLNEAAEKESDTTTAAFAQENIAKYEKSLWMIGATLQGAC 147
               SCOP domains d3kwoa_ A: automated matches                                                                                                                          SCOP domains
               CATH domains 3kwoA00 A:-1-147  [code=1.20.1260.10, no name defined]                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kwo A  -1 NAmSVTKQLLQmQADAHHLWVKFHNYHWNVKGLQFFSIHEYTEKAYEEmAELFDSCAERVLQLGEKAITCQKVLmENAKSPKVAKDCFTPLEVIELIKQDYEYLLAEFKKLNEAAEKESDTTTAAFAQENIAKYEKSLWmIGATLQGAC 147
                              |      8 |      18        28        38        48        58        68    |   78        88        98       108       118       128       138         
                              |       10-MSE                               47-MSE                    73-MSE                                                          138-MSE     
                              1-MSE                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:147
 aligned with DPS_CAMJE | Q0P891 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
            DPS_CAMJE     1 MSVTKQLLQMQADAHHLWVKFHNYHWNVKGLQFFSIHEYTEKAYEEMAELFDSCAERVLQLGEKAITCQKVLMENAKSPKVAKDCFTPLEVIELIKQDYEYLLAEFKKLNEAAEKESDTTTAAFAQENIAKYEKSLWMIGATLQGAC 147
               SCOP domains d3kwob_ B: automated matches                                                                                                                        SCOP domains
               CATH domains -3kwoB00 B:2-147  [code=1.20.1260.10, no name defined]                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kwo B   1 mSVTKQLLQmQADAHHLWVKFHNYHWNVKGLQFFSIHEYTEKAYEEmAELFDSCAERVLQLGEKAITCQKVLmENAKSPKVAKDCFTPLEVIELIKQDYEYLLAEFKKLNEAAEKESDTTTAAFAQENIAKYEKSLWmIGATLQGAC 147
                            |       10        20        30        40      | 50        60        70  |     80        90       100       110       120       130       140       
                            1-MSE   10-MSE                               47-MSE                    73-MSE                                                          138-MSE     


Chain C from PDB  Type:PROTEIN  Length:147
 aligned with DPS_CAMJE | Q0P891 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
            DPS_CAMJE     1 MSVTKQLLQMQADAHHLWVKFHNYHWNVKGLQFFSIHEYTEKAYEEMAELFDSCAERVLQLGEKAITCQKVLMENAKSPKVAKDCFTPLEVIELIKQDYEYLLAEFKKLNEAAEKESDTTTAAFAQENIAKYEKSLWMIGATLQGAC 147
               SCOP domains d3kwoc_ C: automated matches                                                                                                                        SCOP domains
               CATH domains -3kwoC00 C:2-147  [code=1.20.1260.10, no name defined]                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kwo C   1 mSVTKQLLQmQADAHHLWVKFHNYHWNVKGLQFFSIHEYTEKAYEEmAELFDSCAERVLQLGEKAITCQKVLmENAKSPKVAKDCFTPLEVIELIKQDYEYLLAEFKKLNEAAEKESDTTTAAFAQENIAKYEKSLWmIGATLQGAC 147
                            |       10        20        30        40      | 50        60        70  |     80        90       100       110       120       130       140       
                            1-MSE   10-MSE                               47-MSE                    73-MSE                                                          138-MSE     


Chain D from PDB  Type:PROTEIN  Length:148
 aligned with DPS_CAMJE | Q0P891 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:148
                             1                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139        
            DPS_CAMJE     - -MSVTKQLLQMQADAHHLWVKFHNYHWNVKGLQFFSIHEYTEKAYEEMAELFDSCAERVLQLGEKAITCQKVLMENAKSPKVAKDCFTPLEVIELIKQDYEYLLAEFKKLNEAAEKESDTTTAAFAQENIAKYEKSLWMIGATLQGAC 147
               SCOP domains d3kwod_ D: automated matches                                                                                                                         SCOP domains
               CATH domains 3kwoD00 D:0-147  [code=1.20.1260.10, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kwo D   0 AmSVTKQLLQmQADAHHLWVKFHNYHWNVKGLQFFSIHEYTEKAYEEmAELFDSCAERVLQLGEKAITCQKVLmENAKSPKVAKDCFTPLEVIELIKQDYEYLLAEFKKLNEAAEKESDTTTAAFAQENIAKYEKSLWmIGATLQGAC 147
                             |       9|       19        29        39       |49        59        69   |    79        89        99       109       119       129       139        
                             1-MSE   10-MSE                               47-MSE                    73-MSE                                                          138-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  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DPS_CAMJE | Q0P891)
molecular function
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0042262    DNA protection    Any process in which DNA is protected from damage by, for example, oxidative stress.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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