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(-) Description

Title :  ZINC SUBSTITUTED REACTION CENTER OF THE RHODOBACTER SPHAEROIDES
 
Authors :  A. Hardjasa, M. E. P. Murphy
Date :  15 Oct 13  (Deposition) - 05 Feb 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  H,L,M
Keywords :  Zinc Bacteriochlorophyll, Photosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. G. Saer, J. Pan, A. Hardjasa, S. Lin, F. Rosell, A. G. Mauk, N. W. Woodbury, M. E. Murphy, J. T. Beatty
Structural And Kinetic Properties Of Rhodobacter Sphaeroide Photosynthetic Reaction Centers Containing Exclusively Zn-Coordinated Bacteriochlorophyll As Bacteriochlorin Cofactors.
Biochim. Biophys. Acta V. 1837 366 2013
PubMed-ID: 24316146  |  Reference-DOI: 10.1016/J.BBABIO.2013.11.015

(-) Compounds

Molecule 1 - REACTION CENTER H CHAIN
    Chains: H
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Plasmid: PRS1
    Expression System Strain: 2.4.1
    Expression System Taxid: 1063
    Expression System Vector Type: PLASMID
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Strain: 2.4.1
 
Molecule 2 - REACTION CENTER PROTEIN L CHAIN
    Chains: L
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Plasmid: PRS1
    Expression System Strain: 2.4.1
    Expression System Taxid: 1063
    Expression System Vector Type: PLASMID
    Gene: PUFL
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Strain: 2.4.1
    Synonym: PHOTOSYNTHETIC REACTION CENTER L SUBUNIT
 
Molecule 3 - REACTION CENTER PROTEIN M CHAIN
    Chains: M
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Strain: 2.4.1
    Expression System Taxid: 1063
    Expression System Vector Type: PLASMID
    Gene: PUFM
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Strain: 2.4.1
    Synonym: PHOTOSYNTHETIC REACTION CENTER M SUBUNIT

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (11, 28)

Asymmetric/Biological Unit (11, 28)
No.NameCountTypeFull Name
12GO6Ligand/Ion[METHYL 9-ACETYL-14-ETHYL-20-HYDROXY-4,8,13,18-TETRAMETHYL-3-{3-OXO-3-[(3,7,11,15-TETRAMETHYLHEXADEC-2-EN-1-YL)OXY]PROPYL}-3,4,20,21-TETRADEHYDROPHORBINE-21-CARBOXYLATATO(2-)-KAPPA~4~N~23~,N~24~,N~25~,N~26~]ZINC
2CDL1Ligand/IonCARDIOLIPIN
3FE1Ligand/IonFE (III) ION
4GGD1Ligand/IonNONADEC-10-ENOIC ACID 2-[3,4-DIHYDROXY-6-HYDROXYMETHYL-5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-TETRAHYDRO-PYRAN-2-YLOXY]-1-OCTADEC-9-ENOYLOXYMETHYL-ETHYL ESTER
5GOL7Ligand/IonGLYCEROL
6HTO2Ligand/IonHEPTANE-1,2,3-TRIOL
7LDA5Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
8PC11Ligand/Ion1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
9PO41Ligand/IonPHOSPHATE ION
10SPO1Ligand/IonSPHEROIDENE
11U102Ligand/IonUBIQUINONE-10

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU H:34 , ARG H:37 , LYS H:62 , ASN L:199 , GOL L:311 , ARG M:267 , CDL M:409BINDING SITE FOR RESIDUE GOL H 301
02AC2SOFTWAREALA H:25BINDING SITE FOR RESIDUE GOL H 302
03AC3SOFTWARETRP H:21 , GOL H:304 , GGD H:305BINDING SITE FOR RESIDUE GOL H 303
04AC4SOFTWARETRP H:21 , GOL H:303 , HOH H:501 , GOL L:313BINDING SITE FOR RESIDUE GOL H 304
05AC5SOFTWAREGLN H:32 , TYR H:40 , ASN H:52 , GLY H:54 , GOL H:303 , ALA L:1 , PRO L:28 , PHE L:29 , ARG M:253 , GLY M:257 , U10 M:407BINDING SITE FOR RESIDUE GGD H 305
06AC6SOFTWARETYR L:128 , LEU L:131 , PHE L:146 , ILE L:150 , HIS L:153 , LEU L:154 , 2GO L:305 , 2GO L:307 , PHE M:197 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , LEU M:214 , LDA M:403 , HOH M:513BINDING SITE FOR RESIDUE 2GO L 301
07AC7SOFTWARETYR L:148BINDING SITE FOR RESIDUE LDA L 302
08AC8SOFTWARE2GO M:401BINDING SITE FOR RESIDUE LDA L 303
09AC9SOFTWARESER L:178 , PHE L:179 , U10 L:306BINDING SITE FOR RESIDUE LDA L 304
10BC1SOFTWAREALA L:93 , ALA L:96 , PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , ALA L:120 , PHE L:121 , ALA L:124 , TYR L:148 , 2GO L:301 , 2GO L:307 , TYR M:210 , ALA M:213 , LEU M:214 , TRP M:252 , MET M:256BINDING SITE FOR RESIDUE 2GO L 305
11BC2SOFTWARELEU L:189 , HIS L:190 , LEU L:193 , GLU L:212 , ASP L:213 , PHE L:216 , TYR L:222 , SER L:223 , ILE L:224 , GLY L:225 , THR L:226 , ILE L:229 , LEU L:232 , LDA L:304 , LEU M:47 , LDA M:404 , PC1 M:410BINDING SITE FOR RESIDUE U10 L 306
12BC3SOFTWAREPHE L:97 , ALA L:124 , ILE L:125 , ALA L:127 , TYR L:128 , LEU L:131 , VAL L:157 , TYR L:162 , ASN L:166 , HIS L:168 , HIS L:173 , ALA L:176 , ILE L:177 , SER L:244 , ALA L:245 , CYS L:247 , MET L:248 , 2GO L:301 , 2GO L:305 , TYR M:210 , 2GO M:402BINDING SITE FOR RESIDUE 2GO L 307
13BC4SOFTWAREHIS H:126 , HOH H:506 , TYR L:73 , LYS L:82 , THR M:21BINDING SITE FOR RESIDUE PO4 L 308
14BC5SOFTWAREGLN L:87 , ILE L:91 , TRP L:142BINDING SITE FOR RESIDUE HTO L 309
15BC6SOFTWAREILE L:91BINDING SITE FOR RESIDUE HTO L 310
16BC7SOFTWARETHR H:63 , PHE H:64 , GOL H:301 , HOH H:419 , ALA L:198 , ASN L:199 , PRO L:200 , HOH L:476BINDING SITE FOR RESIDUE GOL L 311
17BC8SOFTWAREALA L:78 , LEU L:80BINDING SITE FOR RESIDUE GOL L 312
18BC9SOFTWAREGOL H:304 , GLN L:62 , LDA M:403BINDING SITE FOR RESIDUE GOL L 313
19CC1SOFTWAREHIS L:168 , MET L:174 , ILE L:177 , SER L:178 , THR L:182 , LDA L:303 , LEU M:160 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , 2GO M:402 , 2GO M:406 , SPO M:408 , HOH M:510BINDING SITE FOR RESIDUE 2GO M 401
20CC2SOFTWARETYR L:162 , PHE L:181 , 2GO L:307 , LEU M:156 , THR M:186 , ASN M:187 , PHE M:189 , SER M:190 , LEU M:196 , PHE M:197 , HIS M:202 , SER M:205 , ILE M:206 , TYR M:210 , GLY M:280 , ILE M:284 , 2GO M:401 , 2GO M:406 , PC1 M:410BINDING SITE FOR RESIDUE 2GO M 402
21CC3SOFTWARETRP L:151 , 2GO L:301 , GOL L:313 , PRO M:200 , LEU M:204BINDING SITE FOR RESIDUE LDA M 403
22CC4SOFTWAREU10 L:306 , PHE M:7 , LEU M:38 , TRP M:41BINDING SITE FOR RESIDUE LDA M 404
23CC5SOFTWAREHIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266BINDING SITE FOR RESIDUE FE M 405
24CC6SOFTWAREPHE L:181 , LEU L:185 , LEU L:189 , GLY M:63 , PHE M:67 , ALA M:125 , VAL M:126 , TRP M:129 , ALA M:149 , PHE M:150 , ALA M:153 , ALA M:273 , THR M:277 , 2GO M:401 , 2GO M:402BINDING SITE FOR RESIDUE 2GO M 406
25CC7SOFTWAREGGD H:305 , PHE L:29 , TRP L:100 , MET M:218 , HIS M:219 , THR M:222 , ALA M:248 , ALA M:249 , TRP M:252 , MET M:256 , ASN M:259 , ALA M:260 , ILE M:265 , TRP M:268BINDING SITE FOR RESIDUE U10 M 407
26CC8SOFTWAREPHE M:67 , ILE M:70 , GLY M:71 , TRP M:75 , TRP M:115 , SER M:119 , PHE M:120 , TRP M:157 , GLY M:161 , TRP M:171 , GLY M:178 , ILE M:179 , HIS M:182 , 2GO M:401BINDING SITE FOR RESIDUE SPO M 408
27CC9SOFTWAREALA H:16 , PHE H:20 , PHE H:23 , GLY H:26 , TYR H:30 , GOL H:301 , HOH H:401 , ASN L:199 , PRO L:200 , GLY M:143 , LYS M:144 , HIS M:145 , TRP M:148 , ARG M:267 , TRP M:271 , LEU M:278 , HOH M:584BINDING SITE FOR RESIDUE CDL M 409
28DC1SOFTWAREVAL L:220 , U10 L:306 , SER M:30 , GLY M:31 , VAL M:32 , GLY M:33 , LEU M:52 , 2GO M:402BINDING SITE FOR RESIDUE PC1 M 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N7K)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Tyr H:40 -Pro H:41
2Val H:75 -Pro H:76
3Ala H:138 -Gly H:139
4Arg H:248 -Lys H:249
5Gly M:48 -Pro M:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N7K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N7K)

(-) Exons   (0, 0)

(no "Exon" information available for 4N7K)

(-) 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 H from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains d4n7kh1 H:11-35          d4n7kh2 H:36-251 automated matches                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..........................eeeee....eeeee...........eee........eee..hhhhhhhhhhh.................eee.hhh...eeee.......eeee....eeeeeeeeeee....eeeeeeeee....eeeee.hhhee....eee...hhhhh............hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n7k H  11 DLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKSV 251
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 


Chain L from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4n7kl_ L: L (light) subunit                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..............ee..eehhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n7k L   1 ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING 281
                                    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 


Chain M from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4n7km_ M: M (medium) subunit                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee........................hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.........hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n7k M   1 AEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHGM 303
                                    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
   Legend:   → Mismatch (orange background)
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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  (4, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N7K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N7K)

(-) Gene Ontology  (13, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala H:138 - Gly H:139   [ RasMol ]  
    Arg H:248 - Lys H:249   [ RasMol ]  
    Gly M:48 - Pro M:49   [ RasMol ]  
    Tyr H:40 - Pro H:41   [ RasMol ]  
    Val H:75 - Pro H:76   [ RasMol ]  
 

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

UniProtKB/Swiss-Prot
        RCEH_RHOSH | P0C0Y7: 1aig 1aij 1ds8 1dv3 1dv6 1e14 1e6d 1f6n 1fnp 1fnq 1jgw 1jgx 1jgy 1jgz 1jh0 1k6l 1k6n 1kby 1l9b 1l9j 1m3x 1mps 1ogv 1pcr 1pss 1pst 1qov 1rg5 1rgn 1rqk 1rvj 1ry5 1rzh 1rzz 1s00 1umx 1yf6 1yst 1z9j 1z9k 2bnp 2bns 2boz 2gmr 2gnu 2hg3 2hg9 2hh1 2hhk 2hit 2hj6 2j8c 2j8d 2jiy 2jj0 2rcr 2uws 2uwt 2uwu 2uwv 2uww 2ux3 2ux4 2ux5 2uxj 2uxk 2uxl 2uxm 2wx5 3dsy 3dta 3dtr 3dts 3du2 3du3 3duq 3i4d 3v3y 3v3z 3zum 3zuw 4h99 4h9l 4hbh 4hbj 4in5 4in6 4in7 4lwy 4n7l 4rcr 4tqq 4v9g 5lse 5v33
        RCEL_RHOSH | P0C0Y8: 1aig 1aij 1ds8 1dv3 1dv6 1e14 1e6d 1f6n 1fnp 1fnq 1jgw 1jgx 1jgy 1jgz 1jh0 1k6l 1k6n 1kby 1l9b 1l9j 1m3x 1mps 1ogv 1pcr 1pss 1pst 1qov 1rg5 1rgn 1rqk 1rvj 1ry5 1rzh 1rzz 1s00 1umx 1yf6 1yst 1z9j 1z9k 2bnp 2bns 2boz 2gmr 2gnu 2hg3 2hg9 2hh1 2hhk 2hit 2hj6 2j8c 2j8d 2jiy 2jj0 2rcr 2uws 2uwt 2uwu 2uwv 2uww 2ux3 2ux4 2ux5 2uxj 2uxk 2uxl 2uxm 2wx5 3dsy 3dta 3dtr 3dts 3du2 3du3 3duq 3i4d 3v3y 3v3z 3zum 3zuw 4h99 4h9l 4hbh 4hbj 4in5 4in6 4in7 4lwy 4n7l 4rcr 4tqq 4v9g 5lse 5v33
        RCEM_RHOSH | P0C0Y9: 1aig 1aij 1ds8 1dv3 1dv6 1e14 1e6d 1f6n 1fnp 1fnq 1jgw 1jgx 1jgy 1jgz 1jh0 1k6l 1k6n 1kby 1l9b 1l9j 1m3x 1mps 1ogv 1pcr 1pss 1pst 1qov 1rg5 1rgn 1rqk 1rvj 1ry5 1rzh 1rzz 1s00 1umx 1yf6 1yst 1z9j 1z9k 2bnp 2bns 2boz 2gmr 2gnu 2hg3 2hg9 2hh1 2hhk 2hit 2hj6 2j8c 2j8d 2jiy 2jj0 2rcr 2uws 2uwt 2uwu 2uwv 2uww 2ux3 2ux4 2ux5 2uxj 2uxk 2uxl 2uxm 2wx5 3dsy 3dta 3dtr 3dts 3du2 3du3 3duq 3i4d 3v3y 3v3z 3zum 3zuw 4h99 4h9l 4hbh 4hbj 4in5 4in6 4in7 4lwy 4n7l 4rcr 4tqq 4v9g 5lse 5v33

(-) Related Entries Specified in the PDB File

2j8c 4n7l