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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ENGINEERED CYTOCHROME CB562 THAT FORMS 2D, ZN-MEDIATED SHEETS
 
Authors :  J. B. Brodin, F. A. Tezcan
Date :  05 Sep 11  (Deposition) - 04 Jul 12  (Release) - 04 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Four Helix Bundle, Electron Transfer, Periplasmic Space, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Brodin, X. I. Ambroggio, C. Tang, K. N. Parent, T. S. Baker, F. A. Tezcan
Metal-Directed, Chemically Tunable Assembly Of One-, Two- And Three-Dimensional Crystalline Protein Arrays.
Nat Chem V. 4 375 2012
PubMed-ID: 22522257  |  Reference-DOI: 10.1038/NCHEM.1290

(-) Compounds

Molecule 1 - SOLUBLE CYTOCHROME B562
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SOLUBLE CYTOCHROME B562
    Gene: CYBC
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CYTOCHROME B-562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):   CD
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:4 , MET A:7 , ASN A:11 , LEU A:14 , MET A:33 , PRO A:45 , PRO A:46 , PHE A:61 , PHE A:65 , LEU A:68 , GLU A:81 , CYS A:98 , CYS A:101 , HIS A:102 , TYR A:105 , ARG A:106 , HOH A:133 , HOH A:152BINDING SITE FOR RESIDUE HEM A 150
02AC2SOFTWAREGLU B:4 , MET B:7 , MET B:33 , PRO B:45 , PHE B:61 , PHE B:65 , CYS B:98 , CYS B:101 , HIS B:102 , TYR B:105 , ARG B:106 , ASP C:21 , LYS C:85BINDING SITE FOR RESIDUE HEM B 150
03AC3SOFTWAREGLU C:4 , MET C:7 , ASN C:11 , MET C:33 , PRO C:45 , PRO C:46 , PHE C:61 , GLY C:64 , PHE C:65 , LEU C:68 , CYS C:98 , CYS C:101 , HIS C:102 , TYR C:105 , ARG C:106BINDING SITE FOR RESIDUE HEM C 150
04AC4SOFTWAREGLU D:4 , MET D:7 , MET D:33 , PRO D:45 , PRO D:46 , PHE D:61 , PHE D:65 , CYS D:98 , CYS D:101 , HIS D:102 , ARG D:106BINDING SITE FOR RESIDUE HEM D 150
05AC5SOFTWAREHIS A:63 , HIS B:73 , HIS B:77 , GLU B:81BINDING SITE FOR RESIDUE ZN B 107
06AC6SOFTWAREGLU A:49 , HIS A:73 , HIS A:77 , HIS B:63 , ILE B:67BINDING SITE FOR RESIDUE ZN A 107
07AC7SOFTWAREHIS C:63 , HIS D:73 , HIS D:77 , GLU D:81BINDING SITE FOR RESIDUE ZN D 107
08AC8SOFTWAREGLU C:49 , HIS C:73 , HIS C:77 , HIS D:63 , ILE D:67BINDING SITE FOR RESIDUE ZN C 107
09AC9SOFTWAREGLU B:49 , ALA D:1 , ASP D:39 , HOH D:151BINDING SITE FOR RESIDUE ZN D 108
10BC1SOFTWAREALA B:1 , ASP B:39 , GLU D:49 , HOH D:152BINDING SITE FOR RESIDUE ZN B 108

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TOM)

(-) 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:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3toma_ A: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3tom A   1 ADLEDNMETLNDNLKVIEKADNAAQVEKALEKMLAAAADALKATPPKLEDKSPDSPEMRDFRHGFAILMGQIHDAAHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain B from PDB  Type:PROTEIN  Length:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3tomb_ B: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3tom B   1 ADLEDNMETLNDNLKVIEKADNAAQVEKALEKMLAAAADALKATPPKLEDKSPDSPEMRDFRHGFAILMGQIHDAAHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain C from PDB  Type:PROTEIN  Length:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3tomc_ C: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3tom C   1 ADLEDNMETLNDNLKVIEKADNAAQVEKALEKMLAAAADALKATPPKLEDKSPDSPEMRDFRHGFAILMGQIHDAAHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain D from PDB  Type:PROTEIN  Length:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3tomd_ D: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3tom D   1 ADLEDNMETLNDNLKVIEKADNAAQVEKALEKMLAAAADALKATPPKLEDKSPDSPEMRDFRHGFAILMGQIHDAAHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100
   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  (0, 0)

(no "CATH Domain" information available for 3TOM)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (C562_ECOLX | P0ABE7)
molecular function
    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:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0022900    electron transport chain    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: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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  3tom
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  C562_ECOLX | P0ABE7
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 Related Entries

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

UniProtKB/Swiss-Prot
        C562_ECOLX | P0ABE7: 1apc 1lm3 1m6t 1qpu 1qq3 256b 2bc5 2qla 3c62 3c63 3de8 3de9 3foo 3fop 3hni 3hnj 3hnk 3hnl 3iq5 3iq6 3l1m 3m15 3m4b 3m4c 3m79 3nmi 3nmj 3nmk 3tol 3u8p 4ea3 4eiy 4iaq 4iar 4ib4 4je9 4jea 4jeb 4jkv 4l6r 4n6h 4nc3 4ntj 4o9r 4or2 4pxz 4py0 4qim 4qin 4rwa 4rwd 4u9d 4u9e 4yay 4z34 4z35 4z36 4zud 5awi 5bu7 5dhg 5dhh 5iu4 5iu7 5iu8 5iua 5iub 5jtb 5k2a 5k2b 5k2c 5k2d 5l31 5l32 5l7d 5l7i 5ndd 5ndz 5nj6 5tvn 5uen 5uig 5unf 5ung 5unh 5uvi

(-) Related Entries Specified in the PDB File

2bc5 CRYSTAL STRUCTURE OF E. COLI CYTOCHROME B562 WITH ENGINEERED C-TYPE HEME LINKAGES
2qla CRYSTAL STRUCTURE OF A 16-HELIX BUNDLE ARCHITECTURE PRODUCED BY THE ZINC-MEDIATED SELF ASSEMBLY OF FOUR CYTOCHROME CB562 MOLECULES
3tol