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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ENGINEERED ZN-RIDC1 CONSTRUCT WITH FOUR INTERFACIAL DISULFIDE BONDS
 
Authors :  F. A. Tezcan, A. M. Medina-Morales, A. Perez, J. D. Brodin
Date :  26 Feb 13  (Deposition) - 21 Aug 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.22
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Four-Helix Bundle, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Medina-Morales, A. Perez, J. D. Brodin, F. A. Tezcan
In Vitro And Cellular Self-Assembly Of A Zn-Binding Protein Cryptand Via Templated Disulfide Bonds.
J. Am. Chem. Soc. V. 135 12013 2013
PubMed-ID: 23905754  |  Reference-DOI: 10.1021/JA405318D

(-) Compounds

Molecule 1 - SOLUBLE CYTOCHROME B562
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 23-128
    Gene: CYBC
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CYTOCHROME B-562

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO47Ligand/IonSULFATE ION
3ZN4Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:7 , PRO A:46 , PHE A:61 , PHE A:65 , CYS A:98 , CYS A:101 , HIS A:102 , ARG A:106 , HOH A:328 , HOH A:330 , HOH A:355 , HOH A:391BINDING SITE FOR RESIDUE HEM A 201
02AC2SOFTWAREHIS A:73 , HIS A:77 , HIS B:63 , ASP D:74BINDING SITE FOR RESIDUE ZN A 202
03AC3SOFTWAREHOH A:421BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWAREGLU B:4 , MET B:7 , MET B:33 , PRO B:45 , PRO B:46 , PHE B:61 , PHE B:65 , CYS B:98 , CYS B:101 , HIS B:102 , ARG B:106 , HOH B:321 , HOH B:344 , HOH B:355 , HOH B:403BINDING SITE FOR RESIDUE HEM B 201
05AC5SOFTWAREHIS A:63 , HIS B:73 , HIS B:77 , ASP C:74BINDING SITE FOR RESIDUE ZN B 202
06AC6SOFTWAREALA B:38BINDING SITE FOR RESIDUE SO4 B 203
07AC7SOFTWAREGLU C:4 , MET C:7 , GLU C:8 , PRO C:46 , PHE C:61 , CYS C:98 , CYS C:101 , HIS C:102 , ARG C:106 , HOH C:318 , HOH C:335 , HOH C:364 , HOH C:371 , HOH C:373 , HOH C:402 , HOH C:403 , HOH C:429BINDING SITE FOR RESIDUE HEM C 201
08AC8SOFTWAREASP B:74 , HIS C:73 , HIS C:77 , HIS D:63BINDING SITE FOR RESIDUE ZN C 202
09AC9SOFTWAREHIS B:73 , ASP C:74 , HOH C:401 , HOH C:423BINDING SITE FOR RESIDUE SO4 C 203
10BC1SOFTWAREALA C:38 , TRP C:41 , TRP C:66 , ILE C:69 , HOH C:422BINDING SITE FOR RESIDUE SO4 C 204
11BC2SOFTWAREGLU D:4 , MET D:7 , GLU D:8 , MET D:33 , PHE D:61 , PHE D:65 , CYS D:98 , CYS D:101 , HIS D:102 , ARG D:106 , HOH D:319 , HOH D:320 , HOH D:343 , HOH D:427BINDING SITE FOR RESIDUE HEM D 201
12BC3SOFTWAREASP A:74 , HIS C:63 , HIS D:73 , HIS D:77BINDING SITE FOR RESIDUE ZN D 202
13BC4SOFTWAREHIS D:73 , ASP D:74 , HOH D:326 , HOH D:352BINDING SITE FOR RESIDUE SO4 D 203
14BC5SOFTWAREALA C:34 , ALA D:38 , TRP D:41 , TRP D:66BINDING SITE FOR RESIDUE SO4 D 204
15BC6SOFTWAREHIS C:77 , HIS D:59 , HIS D:63 , HOH D:338 , HOH D:357 , HOH D:386BINDING SITE FOR RESIDUE SO4 D 205

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:81 -D:81
2A:96 -C:96
3B:81 -C:81
4B:96 -D:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JEA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JEA)

(-) 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:106
                                                                                                                                          
               SCOP domains d4jeaa_ 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
                 4jea A   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHDALHLANCGKVKEAQAAAEQLKCTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain B from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains d4jeab_ 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
                 4jea B   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHDALHLANCGKVKEAQAAAEQLKCTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain C from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains d4jeac_ C: 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
                 4jea C   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHDALHLANCGKVKEAQAAAEQLKCTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain D from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains d4jead_ 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
                 4jea D   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHDALHLANCGKVKEAQAAAEQLKCTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  4jea
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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 3tom 3u8p 4ea3 4eiy 4iaq 4iar 4ib4 4je9 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 CYTOCHROME B562 WITH ENGINEERED C-TYPE HEME LINKAGES
2qla ZINC-MEDIATED ASSEMBLY OF MBPC1
3hni ZN MEDIATED RIDC1 TETRAMER
3hnk DIMERIC ASSEMBLY OF RIDC1
3iq5 METAL-FREE TETRAMERIC CYTOCHROME CB562 COMPLEX WITH TWO INTERFACIAL DISULFIDE BONDS
3iq6 ZN(II) MEDIATED TETRAMERIC CYTOCHROME CB562 COMPLEX WITH TWO INTERFACIAL DISULFIDE BONDS
4je9 EENGINEERED METAL-FREE RIDC1 CONSTRUCT WITH FOUR INTERFACIAL DISULFIDE BONDS
4jeb ENGINEERED RIDC1 TETRAMER WITH FOUR INTERFACIAL DISULFIDE BONDS AND FOUR THREE-COORDINATE ZN(II) SITES