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(-) Description

Title :  L(M196)H,H(M202)L DOUBLE MUTANT STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES STRAIN RV
 
Authors :  A. G. Gabdulkhakov
Date :  29 Jul 13  (Deposition) - 16 Jul 14  (Release) - 16 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  H,L,M
Keywords :  Photosynthetic Reaction Center, Primary Electron Donor, Photon, Membrane, Electron Transport, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. G. Kljashtorny, T. Y. Fufina, L. G. Vasilieva, A. G. Gabdulkhakov
Molecular Dynamic Studies Of Reaction Centers Mutants From Rhodobacter Sphaeroides And His Mutant Form L(M196)H+H(M202)L
Crystallogr Rep. V. 59 536 2014
PubMed: search

(-) Compounds

Molecule 1 - REACTION CENTER PROTEIN H CHAIN
    Chains: H
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Taxid: 1063
    Gene: PUHA
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Synonym: PHOTOSYNTHETIC REACTION CENTER H SUBUNIT
 
Molecule 2 - REACTION CENTER PROTEIN L CHAIN
    Chains: L
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Taxid: 1063
    Gene: PUFL
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Synonym: PHOTOSYNTHETIC REACTION CENTER L SUBUNIT
 
Molecule 3 - REACTION CENTER PROTEIN M CHAIN
    Chains: M
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Taxid: 1063
    Gene: PUFM
    Mutation: YES
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    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  (13, 45)

Asymmetric/Biological Unit (13, 45)
No.NameCountTypeFull Name
1BCL3Ligand/IonBACTERIOCHLOROPHYLL A
2BPH3Ligand/IonBACTERIOPHEOPHYTIN A
3CDL1Ligand/IonCARDIOLIPIN
4DIO4Ligand/Ion1,4-DIETHYLENE DIOXIDE
5EDO7Ligand/Ion1,2-ETHANEDIOL
6FE1Ligand/IonFE (III) ION
7K1Ligand/IonPOTASSIUM ION
8LDA6Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
9PO43Ligand/IonPHOSPHATE ION
10SPN1Ligand/IonSPEROIDENONE
11TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
12U102Ligand/IonUBIQUINONE-10
13UNL11Ligand/IonUNKNOWN LIGAND

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN H:32 , TYR H:40 , GLN H:53 , PHE H:56 , HOH H:405 , PHE M:258 , U10 M:406 , LDA M:408BINDING SITE FOR RESIDUE LDA H 301
02AC2SOFTWAREHIS H:126 , TYR L:73 , LYS L:82 , THR M:21BINDING SITE FOR RESIDUE PO4 H 306
03AC3SOFTWAREGLU H:94 , PHE H:96 , PHE L:24 , VAL L:26BINDING SITE FOR RESIDUE DIO H 307
04AC4SOFTWAREASN H:52 , GLU H:94 , ALA L:1BINDING SITE FOR RESIDUE EDO H 308
05AC5SOFTWAREARG H:177 , GLN H:194 , GLY M:230BINDING SITE FOR RESIDUE EDO H 309
06AC6SOFTWAREILE H:65 , LEU H:66 , GLY H:69 , ARG H:70 , GLY H:71BINDING SITE FOR RESIDUE EDO H 310
07AC7SOFTWARESER H:80 , ASP H:82 , ALA H:116 , ARG M:241BINDING SITE FOR RESIDUE EDO H 311
08AC8SOFTWAREGLN H:199 , ASN H:201 , ARG H:202BINDING SITE FOR RESIDUE TRS H 312
09AC9SOFTWAREMET H:134 , ALA H:137 , PHE H:140BINDING SITE FOR RESIDUE K H 313
10BC1SOFTWAREHIS L:168 , MET L:174 , ILE L:177 , THR L:178 , PHE L:181 , THR L:182 , U10 L:304 , HOH L:408 , LEU M:160 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , BPH M:402 , BPH M:404 , SPN M:407BINDING SITE FOR RESIDUE BCL L 301
11BC2SOFTWAREPHE L:97 , ALA L:124 , ILE L:125 , ALA L:127 , TYR L:128 , LEU L:131 , VAL L:157 , SER L:158 , PHE L:167 , HIS L:168 , HIS L:173 , ALA L:176 , ILE L:177 , PHE L:180 , SER L:244 , ALA L:245 , CYS L:247 , MET L:248 , BPH L:303 , TYR M:210 , BPH M:402 , BCL M:403 , U10 M:406BINDING SITE FOR RESIDUE BCL L 302
12BC3SOFTWAREPHE L:41 , ALA L:42 , CYS L:92 , ALA 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 , HIS L:153 , VAL L:241 , BCL L:302 , TYR M:210 , ALA M:213 , LEU M:214 , TRP M:252 , MET M:256 , BCL M:403 , U10 M:406BINDING SITE FOR RESIDUE BPH L 303
13BC4SOFTWAREPRO L:171 , THR L:178 , LEU L:189 , HIS L:190 , LEU L:193 , ASP L:213 , PHE L:216 , SER L:223 , ILE L:224 , GLY L:225 , THR L:226 , ILE L:229 , LEU L:232 , BCL L:301 , DIO M:418BINDING SITE FOR RESIDUE U10 L 304
14BC5SOFTWARELYS H:62 , THR H:63 , PHE H:64 , ALA L:198 , ASN L:199 , PRO L:200BINDING SITE FOR RESIDUE DIO L 309
15BC6SOFTWARESER L:52 , VAL L:66 , TYR L:67 , LEU L:80 , ALA L:81 , GLY L:83 , LEU L:85BINDING SITE FOR RESIDUE EDO L 311
16BC7SOFTWARETHR H:90 , TRP L:262BINDING SITE FOR RESIDUE TRS L 312
17BC8SOFTWAREALA H:16 , PHE H:20 , PHE H:23 , LEU H:27 , TYR H:30 , ASN L:199 , MET M:142 , GLY M:143 , LYS M:144 , HIS M:145 , TRP M:148 , ARG M:267 , ILE M:270 , LEU M:278BINDING SITE FOR RESIDUE CDL M 401
18BC9SOFTWAREHIS L:168 , PHE L:181 , BCL L:301 , BCL L:302 , MET M:122 , LEU M:156 , TRP M:157 , LEU M:160 , THR M:186 , ASN M:187 , PHE M:189 , SER M:190 , HIS M:196 , PHE M:197 , LEU M:202 , SER M:205 , ILE M:206 , TYR M:210 , VAL M:276 , GLY M:280 , ILE M:284 , BPH M:404BINDING SITE FOR RESIDUE BPH M 402
19CC1SOFTWARETYR L:128 , LEU L:131 , HIS L:153 , LEU L:154 , BCL L:302 , BPH L:303 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , LEU M:214 , LDA M:408BINDING SITE FOR RESIDUE BCL M 403
20CC2SOFTWAREPHE L:181 , ALA L:184 , LEU L:185 , LEU L:189 , LEU L:219 , BCL L:301 , SER M:59 , LEU M:60 , GLY M:63 , TRP M:66 , PHE M:67 , VAL M:126 , TRP M:129 , THR M:146 , ALA M:149 , PHE M:150 , ALA M:153 , ALA M:273 , THR M:277 , BPH M:402BINDING SITE FOR RESIDUE BPH M 404
21CC3SOFTWAREHIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266BINDING SITE FOR RESIDUE FE M 405
22CC4SOFTWARELDA H:301 , PHE L:29 , GLY L:35 , TRP L:100 , BCL L:302 , BPH L:303 , 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:268 , MET M:272BINDING SITE FOR RESIDUE U10 M 406
23CC5SOFTWAREBCL L:301 , PHE M:67 , PHE M:68 , ILE M:70 , GLY M:71 , TRP M:75 , TRP M:115 , SER M:119 , PHE M:120 , MET M:122 , PHE M:123 , TRP M:157 , GLY M:161 , PHE M:162 , TRP M:171 , TYR M:177 , GLY M:178 , ILE M:179 , HIS M:182BINDING SITE FOR RESIDUE SPN M 407
24CC6SOFTWARETRP H:21 , LDA H:301 , PRO M:200 , LEU M:204 , MET M:272 , BCL M:403BINDING SITE FOR RESIDUE LDA M 408
25CC7SOFTWAREPHE M:7 , LEU M:38 , TRP M:41BINDING SITE FOR RESIDUE LDA M 409
26CC8SOFTWAREVAL L:220 , GLY L:221 , SER M:30 , GLY M:31 , VAL M:32 , GLY M:33 , GLY M:48BINDING SITE FOR RESIDUE LDA M 410
27CC9SOFTWAREPHE M:105 , ALA M:106 , ALA M:107 , LEU M:109BINDING SITE FOR RESIDUE LDA M 411
28DC1SOFTWAREGLY L:57 , ARG M:13 , GLY M:33 , PRO M:34 , PHE M:35 , THR M:37BINDING SITE FOR RESIDUE LDA M 412
29DC2SOFTWAREASN M:28 , TYR M:51 , GLY M:53 , SER M:54BINDING SITE FOR RESIDUE PO4 M 416
30DC3SOFTWARETYR M:3 , GLN M:4 , ASN M:5 , ILE M:6 , PHE M:7BINDING SITE FOR RESIDUE PO4 M 417
31DC4SOFTWARETRP L:266 , U10 L:304 , PHE M:90BINDING SITE FOR RESIDUE DIO M 418
32DC5SOFTWARELEU H:241 , ILE L:113 , TYR L:115 , GLU M:2 , ARG M:228BINDING SITE FOR RESIDUE EDO M 419
33DC6SOFTWAREGLN H:194 , HIS L:116 , TYR M:3 , GLN M:4 , LEU M:224 , ALA M:225 , SER M:227 , ARG M:228BINDING SITE FOR RESIDUE EDO M 420

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr H:40 -Pro H:41
2Val H:75 -Pro H:76
3Gly M:48 -Pro M:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LWY)

(-) 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:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..........................eeee......eeee...........eee........eee..hhhhhhhhhhh.................eee.......eeee.......eeee....eeeeeeeeeee....eeeeeeee.....eeeee.hhhee....eee....................hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lwy H  11 DLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKS 250
                                    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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.......hhhhh..ee..ee.hhhhhhhhhhhhhhhhhhhhhh................hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lwy L   1 ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAITFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee......................hhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh........hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lwy M   1 AEYQNIFTQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNHFYNPFLGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHG 302
                                    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  (0, 0)

(no "SCOP Domain" information available for 4LWY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    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 4n7k 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 4n7k 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 4n7k 4n7l 4rcr 4tqq 4v9g 5lse 5v33

(-) Related Entries Specified in the PDB File

3v3y PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES STRAIN RV
3v3z I(L177)H MUTANT STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES