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(-) Description

Title :  STRUCTURE DETERMINATION OF A 16.8KDA COPPER PROTEIN RUSTICYANIN AT 2.1A RESOLUTION USING ANOMALOUS SCATTERING DATA WITH DIRECT METHODS
 
Authors :  I. Harvey, Q. Hao, E. M. H. Duke, W. J. Ingledew, S. S. Hasnain
Date :  30 Mar 98  (Deposition) - 17 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Direct Methods, Sas, Medium Resolution, Metalloprotein, Copper Protein, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Harvey, Q. Hao, E. M. Duke, W. J. Ingledew, S. S. Hasnain
Structure Determination Of A 16. 8 Kda Copper Protein At 2. 1 A Resolution Using Anomalous Scattering Data With Direct Methods.
Acta Crystallogr. , Sect. D V. 54 629 1998
PubMed-ID: 9761859  |  Reference-DOI: 10.1107/S0907444998005423
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RUSTICYANIN
    Cellular Location: PERIPLASM
    Chains: A
    Organism Scientific: ACIDITHIOBACILLUS FERROOXIDANS
    Organism Taxid: 920
    Other Details: REDUCED FORM (CU(I))

 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:85 , CYS A:138 , HIS A:143 , MET A:148BINDING SITE FOR RESIDUE CU1 A 156

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A8Z)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:51 -Pro A:52
2Pro A:94 -Pro A:95
3Asp A:103 -Pro A:104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A8Z)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COPPER_BLUEPS00196 Type-1 copper (blue) proteins signature.RUS_ACIF2163-180  1A:131-148
RUS2_ACIFR163-180  1A:131-148
2MULTICOPPER_OXIDASE1PS00079 Multicopper oxidases signature 1.RUS_ACIF2164-184  1A:132-152
RUS2_ACIFR164-184  1A:132-152

(-) Exons   (0, 0)

(no "Exon" information available for 1A8Z)

(-) 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 d1a8za_ A: Rusticyanin                                                                                                                                    SCOP domains
               CATH domains 1a8zA00 A:3-155 Cupredoxins -  blue copper proteins                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeehhhhhhhhhh...eee..eee....eeeeeeee.........eee......eeee....eeeeeeee.........eee..............eeee..........eeeeeeeee....eeeeee...........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------COPPER_BLUE       ------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1 --- PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a8z A   3 LDTSWKEATLPQVKAMLQKDTGKVSGDTVTYSGKTVHVVAAAVLPGFPFPSFEVHDKKNPTLDIPAGATVDVTFINTNKGFGHSFDITQKTPPFAVMPVIDPIVAGTGFSPVPKDGKFGYTNFTWHPTAGTYYYVCQIPGHAATGMFGKIVVK 155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152   


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 d1a8za_ A: Rusticyanin                                                                                                                                    SCOP domains
               CATH domains 1a8zA00 A:3-155 Cupredoxins -  blue copper proteins                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeehhhhhhhhhh...eee..eee....eeeeeeee.........eee......eeee....eeeeeeee.........eee..............eeee..........eeeeeeeee....eeeeee...........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------COPPER_BLUE       ------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1 --- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a8z A   3 LDTSWKEATLPQVKAMLQKDTGKVSGDTVTYSGKTVHVVAAAVLPGFPFPSFEVHDKKNPTLDIPAGATVDVTFINTNKGFGHSFDITQKTPPFAVMPVIDPIVAGTGFSPVPKDGKFGYTNFTWHPTAGTYYYVCQIPGHAATGMFGKIVVK 155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152
   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 1A8Z)

(-) 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).

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  1a8z
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1A8Z)