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(-) Description

Title :  WILD-TYPE PAS-GAF FRAGMENT FROM DEINOCOCCUS RADIODURANS BPHP COLLECTED AT SACLA
 
Authors :  P. Edlund, E. Claesson, T. Nakane, H. Takala, R. Dods, M. Schmidt, S. Wes
Date :  17 Jun 16  (Deposition) - 26 Oct 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, Photosensor, Transferase, Phytochrome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Edlund, H. Takala, E. Claesson, L. Henry, R. Dods, H. Lehtivuori, M. Panman, K. Pande, T. White, T. Nakane, O. Berntsson, E. Gustavsson, P. Bath, V. Modi, S. Roy-Chowdhury, J. Zook, P. Berntsen, S. Pandey, I. Poudyal, J. Tenboer, C. Kupitz, A. Barty, P. Fromme, J. D. Koralek, T. Tanaka, J. Spence, M. Liang, M. S. Hunter, S. Boutet, E. Nango, K. Moffat, G. Groenhof, J. Ihalainen, E. A. Stojkovic, M. Schmidt, S. Westenhoff
The Room Temperature Crystal Structure Of A Bacterial Phytochrome Determined By Serial Femtosecond Crystallography.
Sci Rep V. 6 35279 2016
PubMed-ID: 27756898  |  Reference-DOI: 10.1038/SREP35279

(-) Compounds

Molecule 1 - BACTERIOPHYTOCHROME
    Atcc: 13939
    Chains: A
    EC Number: 2.7.13.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BPHP, DR_A0050
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
    Synonym: PHYTOCHROME-LIKE PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2LBV1Ligand/Ion3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:24 , MET A:174 , TYR A:176 , PHE A:203 , ASP A:207 , ILE A:208 , PRO A:209 , TYR A:216 , ARG A:254 , THR A:256 , SER A:257 , HIS A:260 , TYR A:263 , SER A:272 , SER A:274 , HIS A:290 , HOH A:527 , HOH A:531 , HOH A:538 , HOH A:547 , HOH A:552 , HOH A:591binding site for residue LBV A 401
2AC2SOFTWAREPHE A:203 , PRO A:204binding site for residue ACT A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LBR)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:235 -Pro A:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LBR)

(-) 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:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh....hhhhhhhh......ee....eeeeee.....eeeee.hhhhhhh.hhhhhh..hhhhhh..hhhhhhhhh.........eeeee....eeeeeeee..eeeeeeee...hhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhh...eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lbr A   7 PFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWPHLSLTVHRVGELLILEFEPTELRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAL 322
                                    16        26        36        46        56        66        76        86        96       106|      119       129||     148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318    
                                                                                                                             106|                 130|                                                                                                                                                                                      
                                                                                                                              110                  140
   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 5LBR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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    Asp A:235 - Pro A:236   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        BPHY_DEIRA | Q9RZA4: 1ztu 2o9b 2o9c 3s7n 3s7o 3s7p 3s7q 4cqh 4ijg 4o01 4o0p 4o8g 4q0h 4q0i 4q0j 4y3i 4y5f 4z1w 4zrr 5ajg 5c5k 5k5b 5l8m 5mg0 5mg1

(-) Related Entries Specified in the PDB File

5k5b SAME CRYSTAL FORM BUT COLLECTED AT 100K
5l8m SAME CRYSTAL FORM BUT COLLECTED AT LCLS