Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT CHLORITE DISMUTASE FROM CANDIDATUS NITROSPIRA DEFLUVII R173E
 
Authors :  K. Gysel, A. Hagmueller, K. Djinovic-Carugo
Date :  01 Aug 13  (Deposition) - 15 Jan 14  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Ferredoxin-Like Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Hofbauer, K. Gysel, M. Bellei, A. Hagmuller, I. Schaffner, G. Mlynek, J. Kostan, K. F. Pirker, H. Daims, P. G. Furtmuller, G. Battistuzzi, K. Djinovic-Carugo, C. Obinger
Manipulating Conserved Heme Cavity Residues Of Chlorite Dismutase: Effect On Structure, Redox Chemistry, And Reactivity.
Biochemistry V. 53 77 2014
PubMed-ID: 24364531  |  Reference-DOI: 10.1021/BI401042Z

(-) Compounds

Molecule 1 - CHLORITE DISMUTASE
    Chains: A, B, C, D, E
    EC Number: 1.13.11.49
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B STREP TEV
    Expression System Strain: BL21(DE3) TUNER
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 27-264
    Gene: CLD, CLD1, NIDE1387
    Mutation: YES
    Organism Scientific: CANDIDATUS NITROSPIRA DEFLUVII
    Organism Taxid: 330214

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3HEM5Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:108 , THR A:109 , TYR A:110 , VAL A:111 , ILE A:139 , LYS A:141 , TRP A:145 , HIS A:160 , THR A:161 , ALA A:164 , PHE A:186 , THR A:188 , PHE A:190 , LEU A:201 , LEU A:205 , PHE A:217BINDING SITE FOR RESIDUE HEM A 301
2AC2SOFTWAREPRO B:108 , THR B:109 , TYR B:110 , VAL B:111 , ILE B:139 , LYS B:141 , TRP B:145 , MET B:157 , HIS B:160 , THR B:161 , ALA B:164 , PHE B:186 , PHE B:190 , LEU B:201 , LEU B:205 , GLU B:210 , PHE B:217BINDING SITE FOR RESIDUE HEM B 301
3AC3SOFTWARELYS B:140 , ARG B:216 , HOH B:406 , HIS D:219BINDING SITE FOR RESIDUE ACT B 302
4AC4SOFTWAREPRO C:108 , THR C:109 , TYR C:110 , VAL C:111 , LEU C:122 , ILE C:139 , LYS C:141 , TRP C:145 , MET C:157 , HIS C:160 , THR C:161 , ALA C:164 , LEU C:168 , PHE C:186 , PHE C:190 , LEU C:205 , PHE C:217 , HOH C:414BINDING SITE FOR RESIDUE HEM C 301
5AC5SOFTWAREGLU C:39BINDING SITE FOR RESIDUE EDO C 302
6AC6SOFTWAREPRO D:108 , THR D:109 , TYR D:110 , VAL D:111 , ILE D:139 , LYS D:141 , MET D:157 , HIS D:160 , THR D:161 , ALA D:164 , PHE D:186 , PHE D:190 , LEU D:201 , LEU D:205 , PHE D:217BINDING SITE FOR RESIDUE HEM D 301
7AC7SOFTWARELYS D:140 , ARG D:216 , HIS E:219BINDING SITE FOR RESIDUE ACT D 302
8AC8SOFTWAREPRO E:108 , THR E:109 , TYR E:110 , ILE E:139 , LYS E:141 , TRP E:145 , MET E:157 , HIS E:160 , THR E:161 , ALA E:164 , LEU E:168 , PHE E:186 , THR E:188 , PHE E:190 , LEU E:205 , PHE E:217BINDING SITE FOR RESIDUE HEM E 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M05)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1His A:219 -Pro A:220
2His B:219 -Pro B:220
3His C:219 -Pro C:220
4His D:219 -Pro D:220
5His E:219 -Pro E:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M05)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M05)

(-) Exons   (0, 0)

(no "Exon" information available for 4M05)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.........eeeeeee.hhhhhhhhhhhhhhh.hhh.eeeeeeeeeee....hhhhhhhhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee.hhhhhhhhhhhhhh.hhhh.eeee....eeeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m05 A   1 ADREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEWWALDQEARTALMQEHTQAALPYLKTVKEKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        


Chain B from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.........eeeeeee.hhhhhhhhhhhhh...hhh.eeeeeeeeee.....hhhhhhhhhhhhhhh........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee.hhhhhhhhhhhhhh.hhhh.eeee....eeeeeehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4m05 B  -1 AMADREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEWWALDQEARTALMQEHTQAALPYLKTVKEKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238


Chain C from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh......eeeeeeeee.......hhhhhhhhhhhhhhhhhhhh...eeeeee.........eeeeeee.hhhhhhhhhhhhhhh.hhh.eeeeeeeeee.....hhhhhhhhhhhhhhh........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhh.hhhh.eeee....eeeeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m05 C   2 DREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEWWALDQEARTALMQEHTQAALPYLKTVKEKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       


Chain D from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.........eeeeeee.hhhhhhhhhhhhhhh.hhh.eeeeeeeeeee....hhhhhhhhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.eeee....eeeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m05 D   1 ADREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEWWALDQEARTALMQEHTQAALPYLKTVKEKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        


Chain E from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.........eeeeeee.hhhhhhhhhhhhhhh.hhh.eeeeeeeeee.....hhhhhhhhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee.hhhhhhhhhhhhhh.hhhh.eeee....eeeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m05 E   2 DREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEWWALDQEARTALMQEHTQAALPYLKTVKEKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
   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  (0, 0)

(no "SCOP Domain" information available for 4M05)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M05)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M05)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    His A:219 - Pro A:220   [ RasMol ]  
    His B:219 - Pro B:220   [ RasMol ]  
    His C:219 - Pro C:220   [ RasMol ]  
    His D:219 - Pro D:220   [ RasMol ]  
    His E:219 - Pro E:220   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4m05
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  B3U4H7_9BACT | B3U4H7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.13.11.49
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  B3U4H7_9BACT | B3U4H7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B3U4H7_9BACT | B3U4H7: 3nn1 3nn2 3nn3 3nn4 4m06 4m07 4m08 4m09

(-) Related Entries Specified in the PDB File

4m06 4m07 4m08 4m09