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(-) Description

Title :  BLASTOCHLORIS VIRIDIS PHOTOSYNTHETIC REACTION CENTER SYNCHROTRON STRUCTURE
 
Authors :  A. S. Sharma, L. Johansson, E. Dunevall, W. Y. Wahlgren, R. Neutze, G. Ka
Date :  28 Oct 16  (Deposition) - 08 Feb 17  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Photosynthetic, Reaction Center, Photosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Sharma, L. Johansson, E. Dunevall, W. Y. Wahlgren, R. Neutze, G. Katona
Asymmetry In Serial Femtosecond Crystallography Data.
Acta Crystallogr A Found Adv V. 73 93 2017
PubMed-ID: 28248658  |  Reference-DOI: 10.1107/S2053273316018696

(-) Compounds

Molecule 1 - PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT
    Chains: A
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079
    Synonym: CYTOCHROME C558/C559
 
Molecule 2 - REACTION CENTER PROTEIN L CHAIN
    Chains: B
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079
    Synonym: PHOTOSYNTHETIC REACTION CENTER L SUBUNIT
 
Molecule 3 - REACTION CENTER PROTEIN M CHAIN
    Chains: C
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079
    Synonym: PHOTOSYNTHETIC REACTION CENTER M SUBUNIT
 
Molecule 4 - REACTION CENTER PROTEIN H CHAIN
    Chains: D
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079
    Synonym: PHOTOSYNTHETIC REACTION CENTER H SUBUNIT

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (11, 21)

Asymmetric/Biological Unit (11, 21)
No.NameCountTypeFull Name
1BCL4Ligand/IonBACTERIOCHLOROPHYLL A
2BPB2Ligand/IonBACTERIOPHEOPHYTIN B
3DGA1Ligand/IonDIACYL GLYCEROL
4FE21Ligand/IonFE (II) ION
5FME1Mod. Amino AcidN-FORMYLMETHIONINE
6HEC4Ligand/IonHEME C
7MPG3Ligand/Ion[(Z)-OCTADEC-9-ENYL] (2R)-2,3-BIS(OXIDANYL)PROPANOATE
8MQ71Ligand/IonMENAQUINONE-7
9NS51Ligand/Ion15-CIS-1,2-DIHYDRONEUROSPORENE
10OTP1Ligand/Ion(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYLTRIHYDROGEN DIPHOSPHATE
11PO42Ligand/IonPHOSPHATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:56 , LYS A:57 , ASN A:58 , VAL A:59 , LYS A:60 , VAL A:61 , LEU A:62 , PHE A:70 , MET A:74 , ILE A:77 , THR A:78 , CYS A:87 , CYS A:90 , HIS A:91 , LEU A:96 , TYR A:104 , ALA A:107 , ARG A:108binding site for residue HEC A 401
02AC2SOFTWARETYR A:89 , TYR A:102 , PRO A:103 , VAL A:106 , ALA A:107 , MET A:110 , LEU A:111 , MET A:113 , THR A:114 , CYS A:132 , CYS A:135 , HIS A:136 , PRO A:140 , LEU A:141 , PRO A:142 , LEU A:289 , ARG A:293 , PRO A:301binding site for residue HEC A 402
03AC3SOFTWAREARG A:202 , VAL A:203 , VAL A:204 , PHE A:230 , MET A:233 , SER A:237 , LEU A:240 , CYS A:244 , CYS A:247 , HIS A:248 , PHE A:253 , ARG A:264 , ALA A:267 , TRP A:268 , ARG A:272 , ILE C:189binding site for residue HEC A 403
04AC4SOFTWAREHIS A:124 , THR A:128 , GLY A:129 , LEU A:240 , GLN A:263 , ILE A:266 , ALA A:267 , ILE A:271 , MET A:273 , VAL A:274 , ASP A:304 , CYS A:305 , CYS A:308 , HIS A:309 , THR A:313 , LYS A:314 , PRO A:315binding site for residue HEC A 404
05AC5SOFTWARECYS A:1 , SER B:178 , TRP B:265 , MPG B:306binding site for residue DGA A 405
06AC6SOFTWAREMET B:174 , VAL B:177 , SER B:178 , PHE B:181 , VAL B:182 , MET B:185 , BCL B:302 , MET C:120 , ILE C:158 , ILE C:177 , HIS C:180 , ILE C:181 , LEU C:184 , BCL C:401 , BPB C:402 , NS5 C:405binding site for residue BCL B 301
07AC7SOFTWAREPHE B:97 , PRO B:124 , MET B:127 , VAL B:157 , PHE B:160 , TYR B:162 , TRP B:167 , HIS B:168 , HIS B:173 , SER B:176 , VAL B:177 , PHE B:241 , GLY B:244 , THR B:248 , BCL B:301 , BCL B:303 , BPB B:304 , TYR C:195 , TYR C:208 , BCL C:401binding site for residue BCL B 302
08AC8SOFTWAREPHE B:128 , PHE B:146 , ILE B:150 , HIS B:153 , LEU B:154 , VAL B:157 , BCL B:302 , BPB B:304 , TYR C:195 , GLY C:201 , ILE C:204 , GLY C:205 , TYR C:208 , BCL C:401 , OTP C:406binding site for residue BCL B 303
09AC9SOFTWAREILE B:42 , ILE B:49 , ALA B:96 , PHE B:97 , TRP B:100 , GLU B:104 , VAL B:117 , PHE B:121 , TYR B:148 , GLY B:149 , HIS B:153 , ALA B:237 , PHE B:241 , BCL B:302 , BCL B:303 , TYR C:208 , LEU C:212 , TRP C:250 , ILE C:254binding site for residue BPB B 304
10AD1SOFTWARETRP B:115 , HIS B:116 , LEU B:119 , SER B:238 , ALA C:1 , ASP C:2 , THR C:5 , ILE C:6binding site for residue MPG B 305
11AD2SOFTWAREDGA A:405 , PHE B:179 , VAL B:182 , HIS B:190 , LEU B:193 , SER B:223 , ILE B:224 , GLY B:225 , ILE B:229 , ASN B:239 , MPG C:407binding site for residue MPG B 306
12AD3SOFTWARETYR B:162 , PHE B:181 , BCL B:301 , BCL B:302 , BCL B:303 , PHE C:148 , ALA C:151 , PHE C:154 , VAL C:155 , THR C:185 , PHE C:187 , TYR C:195 , HIS C:200 , SER C:203 , ILE C:204 , TYR C:208 , ALA C:278 , ILE C:282 , BPB C:402binding site for residue BCL C 401
13AD4SOFTWAREPHE B:181 , MET B:185 , LEU B:189 , BCL B:301 , PHE C:59 , SER C:63 , ILE C:66 , LEU C:67 , LEU C:70 , SER C:123 , LEU C:124 , TRP C:127 , ILE C:144 , ASN C:147 , PHE C:148 , SER C:271 , BCL C:401 , NS5 C:405binding site for residue BPB C 402
14AD5SOFTWAREHIS B:190 , HIS B:230 , HIS C:217 , GLU C:232 , HIS C:264binding site for residue FE2 C 403
15AD6SOFTWARETYR B:29 , ILE B:39 , TRP B:100 , ARG B:103 , HIS C:217 , THR C:220 , ALA C:246 , ALA C:247 , TRP C:250 , ILE C:254 , PHE C:256 , ASN C:257 , ALA C:258 , VAL C:263 , TRP C:266binding site for residue MQ7 C 404
16AD7SOFTWAREBCL B:301 , LEU C:70 , GLY C:117 , THR C:121 , GLY C:159 , CYS C:160 , VAL C:173 , PHE C:175 , GLY C:176 , ILE C:177 , HIS C:180 , BPB C:402binding site for residue NS5 C 405
17AD8SOFTWAREPHE B:62 , BCL B:303 , PRO C:198 , PHE C:206 , TRP C:295 , CYS C:296 , ALA C:301 , TRP D:17 , TRP D:25binding site for residue OTP C 406
18AD9SOFTWAREMPG B:306binding site for residue MPG C 407
19AE1SOFTWARETRP C:23 , TYR C:50 , GLY C:52 , ALA C:53 , SER C:54 , SER C:133binding site for residue PO4 C 408
20AE2SOFTWAREASN B:199 , HIS C:143 , ARG C:265binding site for residue PO4 C 409

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M7L)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro A:5 -Pro A:6
2Leu A:152 -Pro A:153
3Gly A:329 -Pro A:330
4Gly C:47 -Pro C:48
5Tyr D:41 -Pro D:42
6Val D:78 -Pro D:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M7L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M7L)

(-) Exons   (0, 0)

(no "Exon" information available for 5M7L)

(-) 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:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee............eehhhhhhhhhhhhh..............hhhhhh.........hhhhhhhhhhhhhhhh....hhhhh..........hhhhhhhhhhhhhhhhhhhhh..........hhhhhh..............................hhhhhhhhhhhh........hhhhhhh.....................hhhhh..hhhhhhhhhhhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..........hhhhhh...hhhhhh.....hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m7l A   1 CFEPPPATTTQTGFRGLSMGEVLHPATVKAKKERDAQYPPALAAVKAEGPPVSQVYKNVKVLGNLTEAEFLRTMTAITEWVSPQEGCTYCHDENNLASEAKYPYVVARRMLEMTRAINTNWTQHVAQTGVTCYTCHRGTPLPPYVRYLEPTLPLNNRETPTHVERVETRSGYVVRLAKYTAYSALNYDPFTMFLANDKRQVRVVPQTALPLVGVSRGKERRPLSDAYATFALMMSISDSLGTNCTFCHNAQTFESWGKKSTPQRAIAWWGIRMVRDLNMNYLAPLNASLPASRLGRQGEAPQADCRTCHQGVTKPLFGASRLKDYPELGPIK 332
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330  


Chain B from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................ee..eehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhh.ee...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m7l B   1 ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS 273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   


Chain C from PDB  Type:PROTEIN  Length:323
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee..............ee...ee..hhhhh...ee..eehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...ee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..............hhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m7l C   1 ADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFAFGSTAILIILFNMAAEVHFDPLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFMTLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGCIHPTLVGSWSEGVPFGIWPHIDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRGTAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHGAAPDYPAYLPATPDPASLPGAPK 323
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320   


Chain D from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhh..............eeee.....eeee...........eee........eee........hhhhh.................eee.......ee..........eee.....eeeeeeeeeee....eeeeeeeee......eeee.hhhee....ee....hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m7l D   1 mYHGALAQHLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVEELPYPKTFVLPHGGTVTVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAERAEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLPVVAADGVEAGTVTDLWVDRSEHYFRYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREEDKVSAYYAGGLLYATPERAESLL 258
                            |       10        20        30        40    ||  65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255   
                            1-FME                                      45|                                                                                                                                                                                                     
                                                                        61
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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 5M7L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M7L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M7L)

(-) Gene Ontology  (17, 47)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYCR_BLAVI | P07173: 1dxr 1prc 1r2c 1vrn 2i5n 2jbl 2prc 2wjm 2wjn 2x5u 2x5v 3d38 3g7f 3prc 3t6d 3t6e 4ac5 4cas 5m7j 5m7k 5prc 6prc 7prc
        RCEH_BLAVI | P06008: 1dxr 1prc 1r2c 1vrn 2i5n 2jbl 2prc 2wjm 2wjn 2x5u 2x5v 3d38 3g7f 3prc 3t6d 3t6e 4ac5 4cas 5m7j 5m7k 5prc 6prc 7prc
        RCEL_BLAVI | P06009: 1dxr 1prc 1r2c 1vrn 2i5n 2jbl 2prc 2wjm 2wjn 2x5u 2x5v 3d38 3g7f 3prc 3t6d 3t6e 4ac5 4cas 5m7j 5m7k 5prc 6prc 7prc
        RCEM_BLAVI | P06010: 1dxr 1prc 1r2c 1vrn 2i5n 2jbl 2prc 2wjm 2wjn 2x5u 2x5v 3d38 3g7f 3prc 3t6d 3t6e 4ac5 4cas 5m7j 5m7k 5prc 6prc 7prc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5M7L)