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(-) Description

Title :  STRUCTURE OF THE PHOTOSENSORY MODULE OF DEINOCOCCUS PHYTOCHROME BY SERIAL FEMTOSECOND X-RAY CRYSTALLOGRAPHY
 
Authors :  E. S. Burgie, F. D. Fuller, S. Gul, I. D. Young, A. S. Brewster, J. Clinger C. Stan, M. Allaire, S. Nelsen, R. Alonso-Mori, G. N. Phillips Jr. , N. J. Kern, V. K. Yachandra, J. Yano, R. D. Vierstra, A. M. Orville
Date :  20 Nov 16  (Deposition) - 22 Feb 17  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Photosensory Module, Phytochrome, Biliverdin, Photoreceptor, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. D. Fuller, S. Gul, R. Chatterjee, E. S. Burgie, I. D. Young, H. Lebrette, V. Srinivas, A. S. Brewster, T. Michels-Clark, J. A. Clinger, B. Andi, M. Ibrahim, E. Pastor, C. De Lichtenberg, R. Hussein, C. J. Pollock, M. Zhang, C. A. Stan, T. Kroll, T. Fransson, C. Weninger, M. Kubin, P. Aller, L. Lassalle, P. Brauer, M. D. Miller, M. Amin, S. Koroidov, C. G. Roessler, M. Allaire, R. G. Sierra, P. T. Docker, J. M. Glownia, S. Nelson, J. E. Koglin, D. Zhu, M. Chollet, S. Song, H. Lemke, M. Liang, D. Sokaras, R. Alonso-Mori, A. Zouni, J. Messinger, U. Bergmann, A. K. Boal, J. M. Bollinger, C. Krebs, M. Hogbom, G. N. Phillips, R. D. Vierstra, N. K. Sauter, A. M. Orville, J. Kern, V. K. Yachandra, J. Yano
Drop-On-Demand Sample Delivery For Studying Biocatalysts In Action At X-Ray Free-Electron Lasers.
Nat. Methods V. 14 443 2017
PubMed-ID: 28250468  |  Reference-DOI: 10.1038/NMETH.4195

(-) Compounds

Molecule 1 - BACTERIOPHYTOCHROME
    Chains: A
    EC Number: 2.7.13.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Gene: BPHP, DR_A0050
    Organism Scientific: DEINOCOCCUS RADIODURANS (STRAIN ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
    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 Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1LBV1Ligand/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
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1LBV2Ligand/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  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:24 , GLU A:27 , ILE A:29 , MET A:174 , PHE A:203 , SER A:206 , ASP A:207 , ILE A:208 , PRO A:209 , TYR A:216 , ARG A:222 , ARG A:254 , SER A:257 , HIS A:260 , TYR A:263 , SER A:272 , SER A:274 , HIS A:290 , HOH A:702 , HOH A:706binding site for residue LBV A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5MG1)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MG1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MG1)

(-) Exons   (0, 0)

(no "Exon" information available for 5MG1)

(-) 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:489
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......hhhhh......ee....eeeeee.....eeeee.hhhhhhh.hhhhhh..hhhhhh..hhhhhhhhh........eeeeeee...eeeeeeee...eeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeee.......eeeeeee............hhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhh...eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhh...eeeeee..eeeeee...hhhhhhhhhhhhh.....eeee.hhhhhh..hhhhh....eeeeee.....eeeeee....eeeeee..hhhhh...........eeeeee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mg1 A   6 LPFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWPGHLSLTVHRVGELLILEFEPTEAGPHALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSLSPHDTLSDPALDLLGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGALVQTDALGQLWPAGADLAPSAAGLLAISVGWSECLVWLRPELRLEVAWGGATPDQAKDDLGPRHSFDTYLEEKRGYAEPWHPGEIEEAQDLRDTLTGAL 502
                                    15        25        35        45        55        65        75        85        95       105||     117       127   ||  141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       433       443       453       463       473       483       493         
                                                                                                                              106|                   131|                                                                                                                                                                                                                                                                                                   430|                                                                     
                                                                                                                               109                    136                                                                                                                                                                                                                                                                                                    433
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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 5MG1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MG1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MG1)

(-) Gene Ontology  (18, 18)

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 Related Entries

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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 5lbr 5mg0

(-) Related Entries Specified in the PDB File

4q0j XFEL DATA VS SYNCHROTRON DATA