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(-) Description

Title :  DEINOCOCCUS RADIODURANS BPHP PAS-GAF
 
Authors :  E. S. Burgie, R. D. Vierstra
Date :  02 Apr 14  (Deposition) - 16 Jul 14  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.16
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Pas Gaf, Photosensor, Response Regulator, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. S. Burgie, T. Wang, A. N. Bussell, J. M. Walker, H. Li, R. D. Vierstra
Crystallographic And Electron Microscopic Analyses Of A Bacterial Phytochrome Reveal Local And Global Rearrangement During Photoconversion.
J. Biol. Chem. V. 289 24573 2014
PubMed-ID: 25006244  |  Reference-DOI: 10.1074/JBC.M114.571661

(-) Compounds

Molecule 1 - BACTERIOPHYTOCHROME
    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: 562
    Expression System Vector Type: PLASMID
    Fragment: PAS-GAF
    Gene: BPHP, DR_A0050
    Mutation: YES
    Organism Scientific: DEINOCOCCUS RADIODURANS R1
    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  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2IPA3Ligand/IonISOPROPYL ALCOHOL
3LBV1Ligand/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 (2, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2IPA6Ligand/IonISOPROPYL ALCOHOL
3LBV2Ligand/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  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:30 , ARG A:218 , PRO A:247 , GLY A:249 , HOH A:552 , HOH A:762BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWAREARG A:172 , HIS A:290BINDING SITE FOR RESIDUE IPA A 402
3AC3SOFTWARETHR A:168 , LEU A:199 , TYR A:295 , IPA A:404 , HOH A:541BINDING SITE FOR RESIDUE IPA A 403
4AC4SOFTWAREGLU A:166 , LEU A:167 , LEU A:199 , GLY A:200 , HIS A:201 , IPA A:403 , HOH A:823BINDING SITE FOR RESIDUE IPA A 404
5AC5SOFTWARECYS A:24 , MET A:174 , TYR A:176 , PHE A:198 , PHE A:203 , SER A:206 , ASP A:207 , ILE A:208 , PRO A:209 , TYR A:216 , ARG A:254 , THR A:256 , SER A:257 , MET A:259 , HIS A:260 , TYR A:263 , MET A:267 , SER A:272 , SER A:274 , HIS A:290 , HOH A:502 , HOH A:504 , HOH A:505 , HOH A:511 , HOH A:514 , HOH A:608BINDING SITE FOR RESIDUE LBV A 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q0H)

(-) 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 4Q0H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q0H)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q0H)

(-) 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:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh.......hhhhh......ee....eeeeee.....eeeee.hhhhhhh.hhhhhh..hhhhhh..hhhhhhhhh.........eeeeee.....eeeeeeeee..eeeeeeeee....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhh...eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q0h A  -1 GSMSRDPLPFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWPAAGHLSLTVHRVGELLILEFEPTEATGPHALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLESLGRLLSLQVQVKEAH 322
                                     8        18        28        38        48        58        68        78        88        98       108       118       128  ||   141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321 
                                                                                                                                                              131|                                                                                                                                                                                           
                                                                                                                                                               135
   Legend:   → Mismatch (orange background)
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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 4Q0H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q0H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q0H)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:235 - Pro A:236   [ RasMol ]  
 
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  4q0h
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  BPHY_DEIRA | Q9RZA4
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  2.7.13.3
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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 4q0i 4q0j 4y3i 4y5f 4z1w 4zrr 5ajg 5c5k 5k5b 5l8m 5lbr 5mg0 5mg1

(-) Related Entries Specified in the PDB File

4q0i 4q0j