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(-) Description

Title :  CRYSTAL STRUCTURE OF A BLUE-LIGHT ABSORBING PROTEORHODOPSIN DOUBLE-MUTANT D97N/Q105L FROM HOT75
 
Authors :  T. Ran, G. Ozorowski, Y. Gao, W. Wang, H. Luecke
Date :  09 May 13  (Deposition) - 05 Jun 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Membrane, Proton Transport, Ion Transport, Proton Pump, Retinylidene Schiff Base (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Ran, G. Ozorowski, Y. Gao, O. A. Sineshchekov, W. Wang, J. L. Spudich H. Luecke
Cross-Protomer Interaction With The Photoactive Site In Oligomeric Proteorhodopsin Complexes.
Acta Crystallogr. , Sect. D V. 69 1965 2013
PubMed-ID: 24100316  |  Reference-DOI: 10.1107/S0907444913017575

(-) Compounds

Molecule 1 - BLUE-LIGHT ABSORBING PROTEORHODOPSIN
    Chains: A, B, C, D, E
    Mutation: YES
    Organism Scientific: GAMMA PROTEOBACTERIUM 'HOT 75M4'
    Organism Taxid: 245185
    Synonym: BPR

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1RET5Ligand/IonRETINAL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:95 , TRP A:98 , THR A:101 , VAL A:102 , MET A:134 , GLY A:138 , TRP A:159 , TRP A:197 , TYR A:200 , TYR A:204 , TYR A:224 , ASP A:228 , LYS A:232BINDING SITE FOR RESIDUE RET A 301
2AC2SOFTWARETRP B:98 , THR B:101 , VAL B:102 , MET B:134 , GLY B:138 , TRP B:197 , TYR B:200 , TYR B:204 , LYS B:232BINDING SITE FOR RESIDUE RET B 301
3AC3SOFTWARETRP C:98 , THR C:101 , VAL C:102 , MET C:134 , GLY C:138 , TRP C:197 , TYR C:200 , TYR C:224 , LYS C:232BINDING SITE FOR RESIDUE RET C 301
4AC4SOFTWARETRP D:98 , THR D:101 , VAL D:102 , MET D:134 , GLY D:138 , GLY D:155 , TRP D:159 , TRP D:197 , TYR D:200 , LYS D:232BINDING SITE FOR RESIDUE RET D 301
5AC5SOFTWARETRP E:98 , THR E:101 , VAL E:102 , MET E:134 , GLY E:138 , TRP E:159 , TRP E:197 , TYR E:200 , LYS E:232BINDING SITE FOR RESIDUE RET E 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4KNF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KNF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KNF)

(-) 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:231
                                                                                                                                                                                                                                                                       
               SCOP domains d4knfa_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4knf A  21 GDLDISDTVGVSFWLVTAGMLAATVFFFVERDQVSAKWKTSLTVSGLITGIAFWHYLYMRGVWIDTGDTPTVFRYINWLLTVPLLVVEFYLILAACTSVAASLFKKLLAGSLVMLGAGFAGEAGLAPVLPAFIIGMAGWLYMIYELYMGEGKAAVSTASPAVNSAYNAMMMIIVVGWAIYPAGYAAGYLMGGGVYASNLNLIYNLADFVNKILFGLIIWNVAVKESSNAKL 252
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 ||    221       231       241       251 
                                                                                                                                                                                                                         212|                                      
                                                                                                                                                                                                                          214                                      


Chain B from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains d4knfb_ B: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4knf B  21 GDLDISDTVGVSFWLVTAGMLAATVFFFVERDQVSAKWKTSLTVSGLITGIAFWHYLYMRGVWIDTGDTPTVFRYINWLLTVPLLVVEFYLIVAASLFKKLLAGSLVMLGAGFAGEAGLAPVLPAFIIGMAGWLYMIYELYMGEGKAAVSSPAVNSAYNAMMMIIVVGWAIYPAGYAAGYLMGVYASNLNLIYNLADFVNKILFGLIIWNVAVKESSNAKLLEH 255
                                    30        40        50        60        70        80        90       100       110 ||    126       136       146       156       166       176|      188       198       208  ||   221       231       241       251    
                                                                                                                     112|                                                      176|                             211|                                        
                                                                                                                      119                                                       179                              215                                        


Chain C from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                        
               SCOP domains d4knfc_ C: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4knf C  21 GDLDISDTVGVSFWLVTAGMLAATVFFFVERDQVSAKWKTSLTVSGLITGIAFWHYLYMRGVWIDTGDTPTVFRYINWLLTVPLLVVEFYLILAACTSVAASLFKKLLAGSLVMLGAGFAGEAGLAPVLPAFIIGMAGWLYMIYELYMGEGKAAVSTASPAVNSAYNAMMMIIVVGWAIYPAGYAAGYLMGGGVYASNLNLIYNLADFVNKILFGLIIWNVAVKESSNAKLL 253
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 ||    221       231       241       251  
                                                                                                                                                                                                                         212|                                       
                                                                                                                                                                                                                          214                                       


Chain D from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains d4knfd_ D: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4knf D  20 GGDLDISDTVGVSFWLVTAGMLAATVFFFVERDQVSAKWKTSLTVSGLITGIAFWHYLYMRGVWIDTGDTPTVFRYINWLLTVPLLVVEFYLILAACTSVAASLFKKLLAGSLVMLGAGFAGEAGLAPVLPAFIIGMAGWLYMIYELYMGEGKAAASPAVNSAYNAMMMIIVVGWAIYPAGYAAGYLMGGVYASNLNLIYNLADFVNKILFGLIIWNVAVKESSNAKLL 253
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169    || 182       192       202       214       224       234       244         
                                                                                                                                                                                    174|                              211|                                       
                                                                                                                                                                                     178                               214                                       


Chain E from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains d4knfe_ E: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4knf E  21 GDLDISDTVGVSFWLVTAGMLAATVFFFVERDQVSAKWKTSLTVSGLITGIAFWHYLYMRGVWIDTGDTPTVFRYINWLLTVPLLVVEFYLILAACTSVAASLFKKLLAGSLVMLGAGFAGEAGLAPVLPAFIIGMAGWLYMIYELYMGEGKAAVSTASPAVNSAYNAMMMIIVVGWAIYPAGYAAGYLMGGVYASNLNLIYNLADFVNKILFGLIIWNVAVKESSNAKL 252
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 ||    222       232       242       252
                                                                                                                                                                                                                         212|                                     
                                                                                                                                                                                                                          215
   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  (1, 5)

Asymmetric/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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        PRRB_PRB02 | Q9AFF7: 4kly

(-) Related Entries Specified in the PDB File

4jq6 4kly