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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF A PUTATIVE CHLORITE DISMUTASE
 
Authors :  M. Gilski, D. Borek, Y. Chen, F. Collart, A. Joachimiak, Z. Otwinowski, Midwest Center For Structural Genomics (Mcsg)
Date :  12 Apr 04  (Deposition) - 24 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  V,W,X,Y,Z
Biol. Unit 1:  V,W,X,Y,Z  (1x)
Biol. Unit 2:  V,W,X,Y,Z  (12x)
Keywords :  Pentamer, Icosahedral, Structural Genomics, Protein Structure Initiative, Mcsg, Psi, Midwest Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Gilski, D. Borek, Y. Chen, F. Collart, A. Joachimiak, Z. Otwinowski
Crystal Structure Of Apc35880 Protein From Bacillus Stearothermophilus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - APC35880
    Chains: V, W, X, Y, Z
    Engineered: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : VWXYZ
Biological Unit 1 (1x): VWXYZ
Biological Unit 2 (12x): VWXYZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1MG5Ligand/IonMAGNESIUM ION
2P335Ligand/Ion3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2P335Ligand/Ion3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
Biological Unit 2 (1, 60)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2P3360Ligand/Ion3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH X:5575 , HOH X:5577 , HOH Z:5837 , HOH Z:5838 , HOH Z:5839 , HOH Z:5840BINDING SITE FOR RESIDUE MG Z 4001
02AC2SOFTWAREHOH W:4252 , HOH W:4253 , HOH W:4254 , HOH Y:5581 , HOH Y:5582 , HOH Y:5583BINDING SITE FOR RESIDUE MG Y 4002
03AC3SOFTWAREHOH V:4258 , HOH V:4259 , HOH W:4255 , HOH W:4256 , HOH W:4257 , HOH W:4258BINDING SITE FOR RESIDUE MG W 4003
04AC4SOFTWAREHOH V:4260 , HOH V:4261 , HOH V:4262 , HOH V:4263 , HOH Z:5841 , HOH Z:5842BINDING SITE FOR RESIDUE MG V 4004
05AC5SOFTWAREHOH X:5599 , HOH X:5600 , HOH X:5601 , HOH X:5602 , HOH Y:5597 , HOH Y:5598BINDING SITE FOR RESIDUE MG X 4005
06AC6SOFTWAREHIS V:171 , GLY V:175 , ALA V:179 , VAL V:182 , GLN V:184 , TRP V:197 , HOH V:4221 , HOH V:4240 , HOH V:4241 , TYR W:113 , SER W:116 , GLY W:117 , GLU W:119BINDING SITE FOR RESIDUE P33 V 1572
07AC7SOFTWARELYS W:148 , HIS W:171 , GLY W:175 , ALA W:179 , VAL W:182 , GLN W:184 , MET W:216 , HOH W:4004 , HOH W:4005 , HOH W:4006 , TYR X:113 , ALA X:115 , SER X:116 , GLY X:117 , GLU X:119 , PRO X:121BINDING SITE FOR RESIDUE P33 W 2572
08AC8SOFTWARETYR V:113 , ALA V:115 , SER V:116 , GLY V:117 , GLU V:119 , HIS X:171 , GLY X:175 , ALA X:179 , VAL X:182 , GLN X:184 , TRP X:197 , HOH X:783 , HOH X:784 , HOH X:909BINDING SITE FOR RESIDUE P33 X 3572
09AC9SOFTWARETYR Y:113 , ALA Y:115 , SER Y:116 , GLY Y:117 , GLU Y:119 , PRO Y:121 , HIS Y:171 , GLY Y:175 , ALA Y:179 , VAL Y:182 , GLN Y:184 , TRP Y:197 , MET Y:216 , HOH Y:252 , HOH Y:282 , HOH Y:875 , HOH Y:989BINDING SITE FOR RESIDUE P33 Y 4572
10BC1SOFTWARESER Z:116 , GLY Z:117 , GLU Z:119 , HIS Z:171 , GLY Z:175 , VAL Z:182 , GLN Z:184 , TRP Z:197 , HOH Z:5578 , HOH Z:5579 , HOH Z:5580 , HOH Z:5811BINDING SITE FOR RESIDUE P33 Z 5572

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T0T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T0T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T0T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T0T)

(-) Exons   (0, 0)

(no "Exon" information available for 1T0T)

(-) 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 V from PDB  Type:PROTEIN  Length:243
 aligned with Y3416_GEOKA | Q5KUD5 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:243
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245   
          Y3416_GEOKA     6 QTLDGWYCLHDFRTIDWSAWKTLPNEEREAAISEFLALVDQWETTESEKQGSHAVYTIVGQKADILFMILRPTLDELHEIETALNKTKLADYLLPAYSYVSVVELSNYLASGSEDPYQIPEVRRRLYPILPKTNYICFYPMDKRRQGNDNWYMLSMEQRRELMRAHGMTGRKYAGKVTQIITGSVGLDDFEWGVTLFSDDALQFKKLVYEMRFDEVSARFGEFGSFFVGTRLSVEKVPSFFHV 248
               SCOP domains d1t0tv_ V: YwfI homologue                                                                                                                                                                                                                           SCOP domains
               CATH domains 1t0tV01 V:6-137 Apc35880; domain 1                                                                                                  1t0tV02 V:138-248 Apc35880; domain 2                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee.........hhhhhhhhhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhh.....eeeeee........eeeeeee..hhhhhhhhhhhhhhhhhhhheee...eeeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0t V   6 QTLDGWYCLHDFRTIDWSAWKTLPNEEREAAISEFLALVDQWETTESEKQGSHAVYTIVGQKADILFMILRPTLDELHEIETALNKTKLADYLLPAYSYVSVVELSNYLASGSEDPYQIPEVRRRLYPILPKTNYICFYPMDKRRQGNDNWYMLSMEQRRELMRAHGMTGRKYAGKVTQIITGSVGLDDFEWGVTLFSDDALQFKKLVYEMRFDEVSARFGEFGSFFVGTRLPMENVSSFFHV 248
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245   


Chain W from PDB  Type:PROTEIN  Length:243
 aligned with Y3416_GEOKA | Q5KUD5 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:243
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245   
          Y3416_GEOKA     6 QTLDGWYCLHDFRTIDWSAWKTLPNEEREAAISEFLALVDQWETTESEKQGSHAVYTIVGQKADILFMILRPTLDELHEIETALNKTKLADYLLPAYSYVSVVELSNYLASGSEDPYQIPEVRRRLYPILPKTNYICFYPMDKRRQGNDNWYMLSMEQRRELMRAHGMTGRKYAGKVTQIITGSVGLDDFEWGVTLFSDDALQFKKLVYEMRFDEVSARFGEFGSFFVGTRLSVEKVPSFFHV 248
               SCOP domains d1t0tw_ W: YwfI homologue                                                                                                                                                                                                                           SCOP domains
               CATH domains 1t0tW01 W:6-137 Apc35880; domain 1                                                                                                  1t0tW02 W:138-248 Apc35880; domain 2                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee.hhhhhhhhhhhhhh.hhhh.eeeeeeeeeeeee.........hhhhhhhhhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhh.....eeeeee........eeeeeee..hhhhhhhhhhhhhhhhhhhheee...eeeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0t W   6 QTLDGWYCLHDFRTIDWSAWKTLPNEEREAAISEFLALVDQWETTESEKQGSHAVYTIVGQKADILFMILRPTLDELHEIETALNKTKLADYLLPAYSYVSVVELSNYLASGSEDPYQIPEVRRRLYPILPKTNYICFYPMDKRRQGNDNWYMLSMEQRRELMRAHGMTGRKYAGKVTQIITGSVGLDDFEWGVTLFSDDALQFKKLVYEMRFDEVSARFGEFGSFFVGTRLPMENVSSFFHV 248
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245   


Chain X from PDB  Type:PROTEIN  Length:243
 aligned with Y3416_GEOKA | Q5KUD5 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:243
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245   
          Y3416_GEOKA     6 QTLDGWYCLHDFRTIDWSAWKTLPNEEREAAISEFLALVDQWETTESEKQGSHAVYTIVGQKADILFMILRPTLDELHEIETALNKTKLADYLLPAYSYVSVVELSNYLASGSEDPYQIPEVRRRLYPILPKTNYICFYPMDKRRQGNDNWYMLSMEQRRELMRAHGMTGRKYAGKVTQIITGSVGLDDFEWGVTLFSDDALQFKKLVYEMRFDEVSARFGEFGSFFVGTRLSVEKVPSFFHV 248
               SCOP domains d1t0tx_ X: YwfI homologue                                                                                                                                                                                                                           SCOP domains
               CATH domains 1t0tX01 X:6-137 Apc35880; domain 1                                                                                                  1t0tX02 X:138-248 Apc35880; domain 2                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee.........hhhhhhhhhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhh.....eeeeee........eeeeeee..hhhhhhhhhhhhhhhhhhhheee...eeeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0t X   6 QTLDGWYCLHDFRTIDWSAWKTLPNEEREAAISEFLALVDQWETTESEKQGSHAVYTIVGQKADILFMILRPTLDELHEIETALNKTKLADYLLPAYSYVSVVELSNYLASGSEDPYQIPEVRRRLYPILPKTNYICFYPMDKRRQGNDNWYMLSMEQRRELMRAHGMTGRKYAGKVTQIITGSVGLDDFEWGVTLFSDDALQFKKLVYEMRFDEVSARFGEFGSFFVGTRLPMENVSSFFHV 248
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245   


Chain Y from PDB  Type:PROTEIN  Length:243
 aligned with Y3416_GEOKA | Q5KUD5 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:243
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245   
          Y3416_GEOKA     6 QTLDGWYCLHDFRTIDWSAWKTLPNEEREAAISEFLALVDQWETTESEKQGSHAVYTIVGQKADILFMILRPTLDELHEIETALNKTKLADYLLPAYSYVSVVELSNYLASGSEDPYQIPEVRRRLYPILPKTNYICFYPMDKRRQGNDNWYMLSMEQRRELMRAHGMTGRKYAGKVTQIITGSVGLDDFEWGVTLFSDDALQFKKLVYEMRFDEVSARFGEFGSFFVGTRLSVEKVPSFFHV 248
               SCOP domains d1t0ty_ Y: YwfI homologue                                                                                                                                                                                                                           SCOP domains
               CATH domains 1t0tY01 Y:6-137 Apc35880; domain 1                                                                                                  1t0tY02 Y:138-248 Apc35880; domain 2                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee.hhhhhhhhhhhhhh.hhhh.eeeeeeeeeeeee.........hhhhhhhhhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhh.....eeeeee........eeeeeee..hhhhhhhhhhhhhhhhhhhheee...eeeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0t Y   6 QTLDGWYCLHDFRTIDWSAWKTLPNEEREAAISEFLALVDQWETTESEKQGSHAVYTIVGQKADILFMILRPTLDELHEIETALNKTKLADYLLPAYSYVSVVELSNYLASGSEDPYQIPEVRRRLYPILPKTNYICFYPMDKRRQGNDNWYMLSMEQRRELMRAHGMTGRKYAGKVTQIITGSVGLDDFEWGVTLFSDDALQFKKLVYEMRFDEVSARFGEFGSFFVGTRLPMENVSSFFHV 248
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245   


Chain Z from PDB  Type:PROTEIN  Length:243
 aligned with Y3416_GEOKA | Q5KUD5 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:243
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245   
          Y3416_GEOKA     6 QTLDGWYCLHDFRTIDWSAWKTLPNEEREAAISEFLALVDQWETTESEKQGSHAVYTIVGQKADILFMILRPTLDELHEIETALNKTKLADYLLPAYSYVSVVELSNYLASGSEDPYQIPEVRRRLYPILPKTNYICFYPMDKRRQGNDNWYMLSMEQRRELMRAHGMTGRKYAGKVTQIITGSVGLDDFEWGVTLFSDDALQFKKLVYEMRFDEVSARFGEFGSFFVGTRLSVEKVPSFFHV 248
               SCOP domains d1t0tz_ Z: YwfI homologue                                                                                                                                                                                                                           SCOP domains
               CATH domains 1t0tZ01 Z:6-137 Apc35880; domain 1                                                                                                  1t0tZ02 Z:138-248 Apc35880; domain 2                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee.........hhhhhhhhhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhh.....eeeeee........eeeeeee..hhhhhhhhhhhhhhhhhhhheee...eeeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0t Z   6 QTLDGWYCLHDFRTIDWSAWKTLPNEEREAAISEFLALVDQWETTESEKQGSHAVYTIVGQKADILFMILRPTLDELHEIETALNKTKLADYLLPAYSYVSVVELSNYLASGSEDPYQIPEVRRRLYPILPKTNYICFYPMDKRRQGNDNWYMLSMEQRRELMRAHGMTGRKYAGKVTQIITGSVGLDDFEWGVTLFSDDALQFKKLVYEMRFDEVSARFGEFGSFFVGTRLPMENVSSFFHV 248
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245
   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, 5)

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

(-) CATH Domains  (2, 10)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1T0T)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain V,W,X,Y,Z   (Y3416_GEOKA | Q5KUD5)
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: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.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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.

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