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(-) Description

Title :  SERIAL FEMTOSECOND CRYSTALLOGRAPHY (SFX) OF GROUND STATE BACTERIORHODOPSIN CRYSTALLIZED FROM BICELLES DETERMINED USING 7-KEV X-RAY FREE ELECTRON LASER (XFEL) AT SACLA
 
Authors :  E. Mizohata, T. Nakane, M. Suzuki
Date :  10 Feb 16  (Deposition) - 09 Nov 16  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Membrane Protein, Proton Pump, Transport Protein, Retinal, Proton Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nakane, S. Hanashima, M. Suzuki, H. Saiki, T. Hayashi, K. Kakinouchi, S. Sugiyama, S. Kawatake, S. Matsuoka, N. Matsumori, E. Nango, J. Kobayashi, T. Shimamura, K. Kimura, C. Mori, N. Kunishima M. Sugahara, Y. Takakyu, S. Inoue, T. Masuda, T. Hosaka, K. Tono, Y. Joti, T. Kameshima, T. Hatsui, M. Yabashi, T. Inoue, O. Nureki, S. Iwata, M. Murata, E. Mizohata
Membrane Protein Structure Determination By Sad, Sir, Or Siras Phasing In Serial Femtosecond Crystallography Using A Iododetergent
Proc. Natl. Acad. Sci. Usa V. 113 13039 2016
PubMed-ID: 27799539  |  Reference-DOI: 10.1073/PNAS.1602531113

(-) Compounds

Molecule 1 - BACTERIORHODOPSIN
    Chains: A
    Organism Scientific: HALOBACTERIUM SALINARUM
    Organism Taxid: 2242
    Strain: R1M1
    Synonym: BR,BACTERIOOPSIN,BO

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 17)

Asymmetric/Biological Unit (8, 17)
No.NameCountTypeFull Name
14QM1Ligand/Ion(3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-DIMETHYL-17-[(2R)-PENTAN-2-YL]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-TETRADECAHYDRO-1H-CYCLOPENTA[A]PHENANTHRENE-3,7,12-TRIOL
2D105Ligand/IonDECANE
3D123Ligand/IonDODECANE
4DD92Ligand/IonNONANE
5HP62Ligand/IonHEPTANE
6OCT1Ligand/IonN-OCTANE
7R162Ligand/IonHEXADECANE
8RET1Ligand/IonRETINAL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:86 , THR A:89 , THR A:90 , LEU A:93 , TRP A:138 , SER A:141 , THR A:142 , TRP A:182 , TYR A:185 , TRP A:189 , ALA A:215 , LYS A:216binding site for residue RET A 301
02AC2SOFTWARELEU A:61 , LEU A:99 , ALA A:103 , ILE A:108binding site for residue 4QM A 302
03AC3SOFTWARED10 A:307binding site for residue OCT A 303
04AC4SOFTWAREARG A:225binding site for residue D10 A 304
05AC5SOFTWAREILE A:203binding site for residue D12 A 305
06AC6SOFTWAREILE A:198 , OCT A:303binding site for residue D10 A 307
07AC7SOFTWARESER A:132 , VAL A:136 , HOH A:428binding site for residue R16 A 309
08AC8SOFTWARED12 A:315binding site for residue D10 A 310
09AC9SOFTWARELYS A:30 , GLY A:65binding site for residue HP6 A 312
10AD1SOFTWARETYR A:147 , DD9 A:316binding site for residue D12 A 314
11AD2SOFTWAREALA A:44 , D10 A:310 , R16 A:317binding site for residue D12 A 315
12AD3SOFTWAREGLY A:106 , LEU A:109 , D12 A:314binding site for residue DD9 A 316
13AD4SOFTWARETRP A:10 , ILE A:11 , D12 A:315binding site for residue R16 A 317

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B35)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:6 -Arg A:7

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B35)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B35)

(-) Exons   (0, 0)

(no "Exon" information available for 5B35)

(-) 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:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b35 A   6 GRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIF 230
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5B35)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B35)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B35)

(-) Gene Ontology  (12, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:6 - Arg A:7   [ RasMol ]  
 

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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 5b6v 5b6w 5b6x 5b6y 5b6z 5br2 5br5 5h2h 5h2i 5h2j 5h2k 5h2l 5h2m 5h2n 5h2o 5h2p 5j7a 5vn7 5vn9
UniProtKB/TrEMBL
        B0R5N9_HALS3 | B0R5N9: 4y9h

(-) Related Entries Specified in the PDB File

5b34