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(-) Description

Title :  DARK-STATE STRUCTURE OF APPA WILD-TYPE WITHOUT THE CYS-RICH REGION FROM RB. SPHAEROIDES
 
Authors :  A. Winkler, U. Heintz, R. Lindner, J. Reinstein, R. Shoeman, I. Schlich
Date :  09 Oct 12  (Deposition) - 05 Jun 13  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Bluf Domain, Schic Domain, Photoreceptor, Ppsr, Flavoprotein, Flavoprotein, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Winkler, U. Heintz, R. Lindner, J. Reinstein, R. L. Shoeman, I. Schlichting
A Ternary Appa-Ppsr-Dna Complex Mediates Light Regulation O Photosynthesis-Related Gene Expression.
Nat. Struct. Mol. Biol. V. 20 859 2013
PubMed-ID: 23728293  |  Reference-DOI: 10.1038/NSMB.2597

(-) Compounds

Molecule 1 - APPA PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 3-399
    Gene: APPA
    Mutation: YES
    Organism Common: RHODOPSEUDOMONAS SPHAEROIDES
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Strain: 2.4.1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:21 , ILE A:37 , SER A:41 , HIS A:44 , ASN A:45 , PHE A:61 , GLN A:63 , LEU A:65 , VAL A:75 , HIS A:78 , ILE A:79 , ASP A:82 , ARG A:84 , MET A:106BINDING SITE FOR RESIDUE FMN A 500
2AC2SOFTWARETYR B:21 , ILE B:37 , SER B:41 , HIS B:44 , ASN B:45 , PHE B:61 , GLN B:63 , VAL B:75 , HIS B:78 , ILE B:79 , ASP B:82 , ARG B:84 , HIS B:85BINDING SITE FOR RESIDUE FMN B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HH1)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg A:124 -Gln A:125
2Arg B:124 -Gln B:125
3Pro B:357 -Gly B:358

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HH1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HH1)

(-) Exons   (0, 0)

(no "Exon" information available for 4HH1)

(-) 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:383
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeeeehhhhhhhhhhhhhh...eeeeeeeeeeee..........eeeeehhhhhhhh.....eee...........hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........eeeeee......hhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh..ee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hh1 A  14 SDLVSCCYRSLAAPDLTLRDLLDIVETSQAHNARAQLTGALFYSQGVFFQWLEGRPAAVAEVMTHIQRDRRHSNVEILAEEPIAKRRFAGWHMQLSCSEADMRSLGLSRQIVTVGRSLVADNTNIFSFDRIAAVRRFLSDVCAARTLAPDTPVEADTFALYALTEAQAGRSGRAKAVARLSDLLSTDPLGRLTEVEELLRAHAPTAADFARLFEACAERLTRALAEDRISRMQVTLAYSALQMALRRIHHLPDPQKSVGAVLVAGVPGHKPILEAALAAEMLRAVGWSTSVVHPESVAALAARLKTSRTSTLVVAPSLLEGTEQEADTLRFVSALRARTDLPGLSILVGGRLAQLPPSKLKDSGADAGFAHLALLPAALARVA 398
                                    23        33        43        53        63        73        83        93       103       113      |125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395   
                                                                                                                                    120|                                                                                                                                                                                                                                                                                   
                                                                                                                                     123                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:382
                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeeeehhhhhhhhhhhhhh...eeeeeeeeeee...........eeeeehhhhhh.......eee...........hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..........eeeee......hhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh...ee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hh1 B  15 DLVSCCYRSLAAPDLTLRDLLDIVETSQAHNARAQLTGALFYSQGVFFQWLEGRPAAVAEVMTHIQRDRRHSNVEILAEEPIAKRRFAGWHMQLSCSEADMRSLGLSRQIVTVGRSLVADNTNIFSFDRIAAVRRFLSDVCAARTLAPDTPVEADTFALYALTEAQAGRSGRAKAVARLSDLLSTDPLGRLTEVEELLRAHAPTAADFARLFEACAERLTRALAEDRISRMQVTLAYSALQMALRRIHHLPDPQKSVGAVLVAGVPGHKPILEAALAAEMLRAVGWSTSVVHPESVAALAARLKTSRTSTLVVAPSLLEGTEQEADTLRFVSALRARTDLPGLSILVGGRLAQLPPSKLKDSGADAGFAHLALLPAALARVA 398
                                    24        34        44        54        64        74        84        94       104       114     ||126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396  
                                                                                                                                   120|                                                                                                                                                                                                                                                                                   
                                                                                                                                    123
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  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 4HH1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HH1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HH1)

(-) Gene Ontology  (4, 4)

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  4hh1
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 Related Entries

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

UniProtKB/TrEMBL
        Q53119_RHOSH | Q53119: 1yrx 2bun 4heh 4hh0 4hh3

(-) Related Entries Specified in the PDB File

1yrx THE BLUF DOMAIN OF APPA FROM RHODOBACTER SPHAEROIDES
2iyg DARK STATE STRUCTURE OF THE APPA BLUF DOMAIN
2iyi LIGHT-INDUCED INTERMEDIATE STRUCTURE OF THE APPA BLUF DOMAIN
4hh0 STRUCTURE OF APPA C20S WITHOUT THE CYS-RICH REGION
4hh2 STRUCTURE OF PPSR WITHOUT THE HTH MOTIF
4hh3 STRUCTURE OF THE APPA PPSR2 CORE COMPLEX