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 HIS143MET RUSTICYANIN
 
Authors :  M. L. Barrett, I. Harvey, M. Sundararajan, R. Surendran, J. F. Hall, M. J M. A. Hough, R. W. Strange, I. H. Hillier, S. S. Hasnain
Date :  21 Dec 05  (Deposition) - 05 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Rusticyanin, Iron Respiratory Electron Transport Chain, Blue Copper Protein, Electron Transport, Metal- Binding, Periplasmic, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Barrett, I. Harvey, M. Sundararajan, R. Surendran, J. F. Hall, M. J. Ellis, M. A. Hough, R. W. Strange, I. H. Hillier, S. S. Hasnain
Atomic Resolution Crystal Structures, Exafs, And Quantum Chemical Studies Of Rusticyanin And Its Two Mutants Provide Insight Into Its Unusual Properties.
Biochemistry V. 45 2927 2006
PubMed-ID: 16503647  |  Reference-DOI: 10.1021/BI052372W

(-) Compounds

Molecule 1 - RUSTICYANIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: THIOBACILLUS FERROOXIDANS
    Organism Taxid: 920

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CU11Ligand/IonCOPPER (I) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:1085 , CYS A:1138 , MET A:1143 , MET A:1148BINDING SITE FOR RESIDUE CU1 A1156

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CAL)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:1051 -Pro A:1052
2Pro A:1094 -Pro A:1095
3Asp A:1103 -Pro A:1104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CAL)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_BLUEPS00196 Type-1 copper (blue) proteins signature.RUS_ACIF2163-180  1A:1131-1148
RUS2_ACIFR163-180  1A:1131-1148
2MULTICOPPER_OXIDASE1PS00079 Multicopper oxidases signature 1.RUS_ACIF2164-184  1A:1132-1152
RUS2_ACIFR164-184  1A:1132-1152

(-) Exons   (0, 0)

(no "Exon" information available for 2CAL)

(-) 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:153
 aligned with RUS2_ACIFR | P0C918 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:153
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184   
          RUS2_ACIFR     35 LDSTWKEATLPQVKAMLEKDTGKVSGDTVTYSGKTVHVVAAAVLPGFPFPSFEVHDKKNPTLEIPAGATVDVTFINTNKGFGHSFDITKKGPPYAVMPVIDPIVAGTGFSPVPKDGKFGYTDFTWHPTAGTYYYVCQIPGHAATGMFGKIIVK  187
               SCOP domains d2cala_ A: automated matches                                                                                                                              SCOP domains
               CATH domains 2calA00 A:1003-1155 Cupredoxins -  blue copper proteins                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeehhhhhhhhhh....eee..eee....eeeeeeee.........eee..ee..eeeee...eeeeeeee.........eee................ee...........eeeeeeee....eeeeee.....hhhhh.eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------COPPER_BLUE       ------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1 --- PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2cal A 1003 LDTTWKEATLPQVKAMLEKDTGKVSGDTVTYSGKTVHVVAAAVLPGFPFPSFEVHDKKNPTLEIPAGATVDVTFINTNKGFGHSFDITKKGPPYAVMPVIDPIVAGTGFSPVPKDGKFGYTDFTWHPTAGTYYYVCQIPGMAATGMFGKIVVK 1155
                                  1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152   


Chain A from PDB  Type:PROTEIN  Length:153
 aligned with RUS_ACIF2 | B7JAQ0 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:153
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184   
           RUS_ACIF2     35 LDTTWKEATLPQVKAMLEKDTGKVSGDTVTYSGKTVHVVAAAVLPGFPFPSFEVHDKKNPTLEIPAGATVDVTFINTNKGFGHSFDITKKGPPYAVMPVIDPIVAGTGFSPVPKDGKFGYTDFTWHPTAGTYYYVCQIPGHAATGMFGKIVVK  187
               SCOP domains d2cala_ A: automated matches                                                                                                                              SCOP domains
               CATH domains 2calA00 A:1003-1155 Cupredoxins -  blue copper proteins                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeehhhhhhhhhh....eee..eee....eeeeeeee.........eee..ee..eeeee...eeeeeeee.........eee................ee...........eeeeeeee....eeeeee.....hhhhh.eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------COPPER_BLUE       ------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1 --- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2cal A 1003 LDTTWKEATLPQVKAMLEKDTGKVSGDTVTYSGKTVHVVAAAVLPGFPFPSFEVHDKKNPTLEIPAGATVDVTFINTNKGFGHSFDITKKGPPYAVMPVIDPIVAGTGFSPVPKDGKFGYTDFTWHPTAGTYYYVCQIPGMAATGMFGKIVVK 1155
                                  1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CAL)

(-) Gene Ontology  (5, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RUS2_ACIFR | P0C918)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain A   (RUS_ACIF2 | B7JAQ0)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 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
    CU1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:1103 - Pro A:1104   [ RasMol ]  
    Phe A:1051 - Pro A:1052   [ RasMol ]  
    Pro A:1094 - Pro A:1095   [ 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
  2cal
    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
  RUS2_ACIFR | P0C918
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  RUS_ACIF2 | B7JAQ0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  RUS2_ACIFR | P0C918
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RUS_ACIF2 | B7JAQ0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RUS2_ACIFR | P0C918: 1a3z 1a8z 1cur 1e30 1gy1 1gy2 1rcy 2cak
        RUS_ACIF2 | B7JAQ0: 1a3z 1a8z 1cur 1e30 1gy1 1gy2 1rcy 2cak

(-) Related Entries Specified in the PDB File

1a3z REDUCED RUSTICYANIN AT 1.9 ANGSTROMS
1a8z STRUCTURE DETERMINATION OF A 16.8KDA COPPER PROTEINRUSTICYANIN AT 2.1A RESOLUTION USING ANOMALOUS SCATTERING DATA WITH DIRECT METHODS
1cur REDUCED RUSTICYANIN, NMR
1e30 CRYSTAL STRUCTURE OF THE MET148GLN MUTANT OF RUSTICYANIN AT 1.5 ANGSTROM RESOLUTION
1gy1 CRYSTAL STRUCTURES OF SER86ASP AND MET148LEU RUSTICYANIN
1gy2 CRYSTAL STRUCTURE OF MET148LEU RUSTICYANIN
1rcy RUSTICYANIN (RC) FROM THIOBACILLUS FERROOXIDANS
2cak 1.27ANGSTROM STRUCTURE OF RUSTICYANIN FROM THIOBACILLUS FERROOXIDANS