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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ENGINEERED PROTEIN THAT FORMS NANOTUBES WITH TUNABLE DIAMETERS
 
Authors :  J. D. Brodin, S. J. Smith, F. A. Tezcan
Date :  03 Jun 15  (Deposition) - 08 Jun 16  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.46
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Metalloprotein, Hemeprotein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Brodin, S. J. Smith, F. A. Tezcan
Designed, Helical Protein Nanotubes With Tunable Diameters From A Single Building Block.
To Be Published
PubMed: search

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ZN7Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:4 , MET A:7 , ASN A:11 , PRO A:46 , PHE A:61 , PHE A:65 , CYS A:98 , CYS A:101 , HIS A:102 , ARG A:106 , HOH B:301binding site for residue HEM A 201
2AC2SOFTWAREALA A:1 , ASP A:39 , ASP B:2 , ASP B:5binding site for residue ZN A 202
3AC3SOFTWAREGLU A:8 , ASP A:12binding site for residue ZN A 203
4AC4SOFTWAREHIS A:73 , ASP A:74 , HIS A:77 , HIS B:63binding site for residue ZN A 204
5AC5SOFTWAREGLU A:27 , GLU A:31 , HIS B:59 , HOH B:319binding site for residue ZN A 205
6AC6SOFTWAREGLU B:4 , MET B:7 , GLU B:8 , PRO B:45 , PHE B:61 , PHE B:65 , CYS B:98 , CYS B:101 , HIS B:102 , TYR B:105 , ARG B:106 , HOH B:301 , HOH B:306 , HOH B:313binding site for residue HEM B 201
7AC7SOFTWAREHIS A:63 , HIS B:73 , ASP B:74 , HIS B:77binding site for residue ZN B 202
8AC8SOFTWAREALA B:1 , ASP B:39 , HOH B:316binding site for residue ZN B 203
9AC9SOFTWAREASP A:54 , HIS A:59 , HOH A:311 , GLU B:27 , GLU B:31binding site for residue ZN B 204

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:96 -B:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5BU7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BU7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BU7)

(-) Exons   (0, 0)

(no "Exon" information available for 5BU7)

(-) 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
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- 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
                 5bu7 A   1 ADLEDNMETLNDNLKVIEKADNAAQVEKALEKMLAAAADALKATPPKLEDKSPDSPEMHDFRHGFAILMGQIHDAAHLANEGKVKEAQAAAEQLKCTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain B from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- 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
                 5bu7 B   1 ADLEDNMETLNDNLKVIEKADNAAQVEKALEKMLAAAADALKATPPKLEDKSPDSPEMHDFRHGFAILMGQIHDAAHLANEGKVKEAQAAAEQLKCTCNACHQKYR 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  (0, 0)

(no "SCOP Domain" information available for 5BU7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BU7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BU7)

(-) Gene Ontology  (7, 7)

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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 4jea 4jeb 4jkv 4l6r 4n6h 4nc3 4ntj 4o9r 4or2 4pxz 4py0 4qim 4qin 4rwa 4rwd 4u9d 4u9e 4yay 4z34 4z35 4z36 4zud 5awi 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 MONOMERIC CYTOCHROME CB562 USED AS THE BASIS FOR DESIGN
2qla ORIGINAL CYTOCHROME CB562 ENGINEERED TO FORM ZN-MEDIATED OLIGOMERS
3tom ENGINEERED CYTOCHROME CB562 THAT FORMS 2D, ZN-MEDIATED SHEETS (DESIGN STARTING POINT)
4jea ENGINEERED CYTOCHROME CB562 STABILIZED BY DISULFIDE BONDS