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(-) Description

Title :  BACTERIORHODOPSIN GROUND STATE STRUCTURE OBTAINED WITH SERIAL FEMTOSECOND CRYSTALLOGRAPHY
 
Authors :  P. Nogly, V. Panneels, G. Nelson, C. Gati, T. Kimura, C. Milne, D. Milath M. Kubo, W. Wu, C. Conrad, J. Coe, R. Bean, Y. Zhao, P. Bath, R. Dods, R. Harimoorthy, K. R. Beyerlein, J. Rheinberger, D. James, D. Deponte L. Sala, G. Williams, M. Hunter, J. E. Koglin, P. Berntsen, E. Nango, S. H. N. Chapman, P. Fromme, M. Frank, R. Abela, S. Boutet, A. Barty, T. A. W U. Weierstall, J. Spence, R. Neutze, G. Schertler, J. Standfuss
Date :  06 Apr 16  (Deposition) - 31 Aug 16  (Release) - 31 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Light-Driven Proton Pump, Retinal Binding, Seven Transmembrane Helix Protein, Proton Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Nogly, V. Panneels, G. Nelson, C. Gati, T. Kimura, C. Milne, D. Milathianaki, M. Kubo, W. Wu, C. Conrad, J. Coe, R. Bean, Y. Zhao, P. Bath, R. Dods, R. Harimoorthy, K. R. Beyerlein, J. Rheinberger, D. James, D. Deponte, C. Li, L. Sala, G. J. Williams, M. S. Hunter, J. E. Koglin, P. Berntsen, E. Nango, S. Iwata, H. N. Chapman, P. Fromme, M. Frank, R. Abela, S. Boutet, A. Barty, T. A. White, U. Weierstall, J. Spence, R. Neutze, G. Schertler, J. Standfuss
Lipidic Cubic Phase Injector Is A Viable Crystal Delivery System For Time-Resolved Serial Crystallography.
Nat Commun V. 7 12314 2016
PubMed-ID: 27545823  |  Reference-DOI: 10.1038/NCOMMS12314
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERIORHODOPSIN
    Chains: A
    Engineered: YES
    Expression System: HALOBACTERIUM SALINARUM
    Expression System Taxid: 2242
    Gene: BOP, VNG_1467G
    Organism Scientific: HALOBACTERIUM SALINARUM (STRAIN ATCC 700922 / JCM 11081 / NRC-1)
    Organism Taxid: 64091
    Strain: ATCC 700922 / JCM 11081 / NRC-1
    Synonym: BR,BACTERIOOPSIN,BO
    Tissue: PURPLE MEMBRANE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1LI15Ligand/Ion1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL
2RET1Ligand/IonRETINAL
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1LI115Ligand/Ion1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL
2RET3Ligand/IonRETINAL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:86 , THR A:90 , TRP A:138 , SER A:141 , THR A:142 , TRP A:182 , TYR A:185 , TRP A:189 , ASP A:212 , LYS A:216binding site for residue RET A 301
2AC2SOFTWARETHR A:24 , LEU A:28 , LYS A:40 , TYR A:147 , LI1 A:305binding site for residue LI1 A 303
3AC3SOFTWARETYR A:64binding site for residue LI1 A 304
4AC4SOFTWARELEU A:58 , LI1 A:303binding site for residue LI1 A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J7A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5J7A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J7A)

(-) Exons   (0, 0)

(no "Exon" information available for 5J7A)

(-) 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:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j7a A   5 TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFG 231
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154|      167       177       187       197       207       217       227    
                                                                                                                                                                               154|                                                                         
                                                                                                                                                                                158
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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 5J7A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J7A)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  5j7a
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  BACR_HALSA | P02945
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 Related Entries

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

UniProtKB/Swiss-Prot
        BACR_HALSA | P02945: 1ap9 1at9 1bac 1bad 1bct 1bha 1bhb 1bm1 1brd 1brr 1brx 1c3w 1c8r 1c8s 1cwq 1dze 1e0p 1f4z 1f50 1fbb 1fbk 1iw6 1iw9 1ixf 1jv6 1jv7 1kg8 1kg9 1kgb 1kme 1l0m 1m0k 1m0l 1m0m 1mgy 1o0a 1p8h 1p8i 1p8u 1pxr 1pxs 1py6 1q5i 1q5j 1qhj 1qko 1qkp 1qm8 1r2n 1r84 1s51 1s52 1s53 1s54 1s8j 1s8l 1tn0 1tn5 1ucq 1vjm 1x0i 1x0k 1x0s 1xji 2at9 2brd 2i1x 2i20 2i21 2ntu 2ntw 2wjk 2wjl 2zfe 2zzl 3coc 3cod 3han 3hao 3hap 3haq 3har 3has 3mbv 3ns0 3nsb 3t45 3utv 3utw 3utx 3uty 3vhz 3vi0 4fpd 4hwl 4hyx 4md1 4md2 4ov0 4x31 4x32 4xxj 5a44 5a45 5b34 5b35 5b6v 5b6w 5b6x 5b6y 5b6z 5br2 5br5 5h2h 5h2i 5h2j 5h2k 5h2l 5h2m 5h2n 5h2o 5h2p 5vn7 5vn9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5J7A)