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(-) Description

Title :  X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBACTER CAPSULATUS AT 2.1 ANGSTROMS
 
Authors :  J. I. Perez-Dorado, J. A. Hermoso, I. Nogues, S. Frago, C. Bittel, S. G. Mayhew, C. Gomez-Moreno, M. Medina, N. Cortez, N. Carrillo
Date :  23 Dec 04  (Deposition) - 07 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Ferredoxin(Flavodoxin)-Nadp(H) Reductase, Flavoproteins, Electron Transfer, Rhodobacter Capsulatus, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Nogues, J. I. Perez-Dorado, S. Frago, C. Bittel, S. G. Mayhew, C. Gomez-Moreno, J. A. Hermoso, M. Medina, N. Cortez, N. Carrillo
The Ferredoxin-Nadp(H) Reductase From Rhodobacter Capsulatus: Molecular Structure And Catalytic Mechanism
Biochemistry V. 44 11730 2005
PubMed-ID: 16128574  |  Reference-DOI: 10.1021/BI0508183
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FERREDOXIN-NADP(H) REDUCTASE
    Chains: A, B, C, D
    EC Number: 1.18.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Mutation: YES
    Organism Scientific: RHODOBACTER CAPSULATUS
    Organism Taxid: 1061
    Strain: 37B4
    Variant: DSM938

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:49 , ARG A:64 , ALA A:65 , TYR A:66 , SER A:67 , TYR A:80 , SER A:81 , ILE A:82 , VAL A:84 , GLY A:87 , PRO A:88 , LEU A:89 , THR A:90 , THR A:130 , ALA A:133 , LYS A:265 , ALA A:266 , PHE A:267 , GLY A:271 , ILE A:272 , HOH A:2021 , HOH A:2028 , HOH A:2040 , HOH A:2085 , HOH A:2086 , HOH A:2090 , HOH A:2091BINDING SITE FOR RESIDUE FAD A1273
2AC2SOFTWAREPHE B:49 , ARG B:64 , ALA B:65 , TYR B:66 , SER B:67 , TYR B:80 , SER B:81 , ILE B:82 , GLY B:87 , PRO B:88 , LEU B:89 , THR B:90 , THR B:130 , ALA B:133 , LYS B:265 , ALA B:266 , PHE B:267 , VAL B:268 , GLU B:270 , GLY B:271 , ILE B:272 , HOH B:2082 , HOH B:2083 , HOH B:2085BINDING SITE FOR RESIDUE FAD B1273
3AC3SOFTWAREARG C:64 , ALA C:65 , TYR C:66 , SER C:67 , TYR C:80 , SER C:81 , ILE C:82 , VAL C:84 , GLY C:87 , PRO C:88 , LEU C:89 , THR C:90 , THR C:130 , ALA C:133 , LYS C:265 , ALA C:266 , PHE C:267 , VAL C:268 , GLU C:270 , GLY C:271 , ILE C:272 , HOH C:2076 , HOH C:2077 , HOH C:2079 , HOH C:2080 , HOH C:2081BINDING SITE FOR RESIDUE FAD C1273
4AC4SOFTWAREARG D:64 , ALA D:65 , TYR D:66 , SER D:67 , TYR D:80 , SER D:81 , ILE D:82 , GLY D:87 , PRO D:88 , LEU D:89 , THR D:90 , THR D:130 , ALA D:133 , LYS D:265 , ALA D:266 , PHE D:267 , VAL D:268 , GLU D:270 , GLY D:271 , ILE D:272 , HOH D:2018 , HOH D:2091 , HOH D:2092 , HOH D:2093 , HOH D:2094BINDING SITE FOR RESIDUE FAD D1273

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BGJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BGJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BGJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BGJ)

(-) Exons   (0, 0)

(no "Exon" information available for 2BGJ)

(-) Sequences/Alignments

Asymmetric 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:260
 aligned with Q9L6V3_RHOCA | Q9L6V3 from UniProtKB/TrEMBL  Length:272

    Alignment length:260
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272
         Q9L6V3_RHOCA    13 KVLPDAQTVTSVRHWTDTLFSFRVTRPQTLRFRSGEFVMIGLLDDNGKPIMRAYSIASPAWDEELEFYSIKVPDGPLTSRLQHIKVGEQIILRPKPVGTLVIDALLPGKRLWFLATGTGIAPFASLMREPEAYEKFDEVIMMHACRTVAELEYGRQLVEALQEDPLIGELVEGKLKYYPTTTREEFHHMGRITDNLASGKVFEDLGIAPMNPETDRAMVCGSLAFNVDVMKVLESYGLREGANSEPREFVVEKAFVGEGI 272
               SCOP domains d2bgja1 A:13-113 automated matches                                                                   d2bgja2 A:114-272 automated matches                                                                                                                             SCOP domains
               CATH domains -------2bgjA01 A:20-106 Translation factors                                                   ------2bgjA02 A:113-266 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                     ------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee..eeeeeee...........eeeeeee.....eeeeeee........eeeeeee......hhhhhh......eeeeeeeee...hhhh.....eeeeeee...hhhhhhhh.hhhhhhhh.eeeeeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeeeee.........hhhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhh............eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bgj A  13 KVLPDAQTVTSVRHWTDTLFSFRVTRPQTLRFRSGEFVMIGLLDDNGKPIMRAYSIASPAWDEELEFYSIKVPDGPLTSRLQHIKVGEQIILRPKPVGTLVIDALLPGKRLWFLATGTGIAPFASLMREPEAYEKFDEVIMMHACRTVAELEYGRQLVEALQEDPLIGELVEGKLKYYPTTTREEFHHMGRITDNLASGKVFEDLGIAPMNPETDRAMVCGSLAFNVDVMKVLESYGLREGANSEPREFVVEKAFVGEGI 272
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272


Chain B from PDB  Type:PROTEIN  Length:257
 aligned with Q9L6V3_RHOCA | Q9L6V3 from UniProtKB/TrEMBL  Length:272

    Alignment length:257
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       
         Q9L6V3_RHOCA    16 PDAQTVTSVRHWTDTLFSFRVTRPQTLRFRSGEFVMIGLLDDNGKPIMRAYSIASPAWDEELEFYSIKVPDGPLTSRLQHIKVGEQIILRPKPVGTLVIDALLPGKRLWFLATGTGIAPFASLMREPEAYEKFDEVIMMHACRTVAELEYGRQLVEALQEDPLIGELVEGKLKYYPTTTREEFHHMGRITDNLASGKVFEDLGIAPMNPETDRAMVCGSLAFNVDVMKVLESYGLREGANSEPREFVVEKAFVGEGI 272
               SCOP domains d2bgjb1 B:16-113 automated matches                                                                d2bgjb2 B:114-272 automated matches                                                                                                                             SCOP domains
               CATH domains ----2bgjB01 B:20-106 Translation factors                                                   ------2bgjB02 B:113-266 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                     ------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee..eeeeeee...........eeeeeee.....eeeeeee........eeeeeee......hhhhhh......eeeeeeeee...hhhh.....eeeeeee...hhhhhhhh.hhhhhhhh.eeeeeeee.hhhhhhhhhhhhhhhhhh.hhhhhh...eeeeeee.........hhhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhh............eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bgj B  16 PDAQTVTSVRHWTDTLFSFRVTRPQTLRFRSGEFVMIGLLDDNGKPIMRAYSIASPAWDEELEFYSIKVPDGPLTSRLQHIKVGEQIILRPKPVGTLVIDALLPGKRLWFLATGTGIAPFASLMREPEAYEKFDEVIMMHACRTVAELEYGRQLVEALQEDPLIGELVEGKLKYYPTTTREEFHHMGRITDNLASGKVFEDLGIAPMNPETDRAMVCGSLAFNVDVMKVLESYGLREGANSEPREFVVEKAFVGEGI 272
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       


Chain C from PDB  Type:PROTEIN  Length:257
 aligned with Q9L6V3_RHOCA | Q9L6V3 from UniProtKB/TrEMBL  Length:272

    Alignment length:257
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       
         Q9L6V3_RHOCA    16 PDAQTVTSVRHWTDTLFSFRVTRPQTLRFRSGEFVMIGLLDDNGKPIMRAYSIASPAWDEELEFYSIKVPDGPLTSRLQHIKVGEQIILRPKPVGTLVIDALLPGKRLWFLATGTGIAPFASLMREPEAYEKFDEVIMMHACRTVAELEYGRQLVEALQEDPLIGELVEGKLKYYPTTTREEFHHMGRITDNLASGKVFEDLGIAPMNPETDRAMVCGSLAFNVDVMKVLESYGLREGANSEPREFVVEKAFVGEGI 272
               SCOP domains d2bgjc1 C:16-113 automated matches                                                                d2bgjc2 C:114-272 automated matches                                                                                                                             SCOP domains
               CATH domains ----2bgjC01 C:20-106 Translation factors                                                   ------2bgjC02 C:113-266 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                     ------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee..eeeeeee...........eeeeeee.....eeeeeee........eeeeeee......hhhhhh......eeeeeeeee...hhhh.....eeeeeee...hhhhhhhh.hhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.........hhhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhh............eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bgj C  16 PDAQTVTSVRHWTDTLFSFRVTRPQTLRFRSGEFVMIGLLDDNGKPIMRAYSIASPAWDEELEFYSIKVPDGPLTSRLQHIKVGEQIILRPKPVGTLVIDALLPGKRLWFLATGTGIAPFASLMREPEAYEKFDEVIMMHACRTVAELEYGRQLVEALQEDPLIGELVEGKLKYYPTTTREEFHHMGRITDNLASGKVFEDLGIAPMNPETDRAMVCGSLAFNVDVMKVLESYGLREGANSEPREFVVEKAFVGEGI 272
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       


Chain D from PDB  Type:PROTEIN  Length:257
 aligned with Q9L6V3_RHOCA | Q9L6V3 from UniProtKB/TrEMBL  Length:272

    Alignment length:257
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       
         Q9L6V3_RHOCA    16 PDAQTVTSVRHWTDTLFSFRVTRPQTLRFRSGEFVMIGLLDDNGKPIMRAYSIASPAWDEELEFYSIKVPDGPLTSRLQHIKVGEQIILRPKPVGTLVIDALLPGKRLWFLATGTGIAPFASLMREPEAYEKFDEVIMMHACRTVAELEYGRQLVEALQEDPLIGELVEGKLKYYPTTTREEFHHMGRITDNLASGKVFEDLGIAPMNPETDRAMVCGSLAFNVDVMKVLESYGLREGANSEPREFVVEKAFVGEGI 272
               SCOP domains d2bgjd1 D:16-113 automated matches                                                                d2bgjd2 D:114-272 automated matches                                                                                                                             SCOP domains
               CATH domains ----2bgjD01 D:20-106 Translation factors                                                   ------2bgjD02 D:113-266 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                     ------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee..eeeeeee...........eeeeeee.....eeeeeee........eeeeeee......hhhhhh......eeeeeeeee...hhhh.....eeeeeee...hhhhhhhh.hhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhh.hhhhhh...eeeeeee.........hhhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhh............eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bgj D  16 PDAQTVTSVRHWTDTLFSFRVTRPQTLRFRSGEFVMIGLLDDNGKPIMRAYSIASPAWDEELEFYSIKVPDGPLTSRLQHIKVGEQIILRPKPVGTLVIDALLPGKRLWFLATGTGIAPFASLMREPEAYEKFDEVIMMHACRTVAELEYGRQLVEALQEDPLIGELVEGKLKYYPTTTREEFHHMGRITDNLASGKVFEDLGIAPMNPETDRAMVCGSLAFNVDVMKVLESYGLREGANSEPREFVVEKAFVGEGI 272
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265
   Legend:   → Mismatch (orange background)
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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  (2, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BGJ)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9L6V3_RHOCA | Q9L6V3)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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        Q9L6V3_RHOCA | Q9L6V3: 2bgi 2vnh 2vni 2vnj 2vnk 4k1x

(-) Related Entries Specified in the PDB File

2bgi X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBACTER CAPSULATUS COMPLEXED WITH THREE MOLECULES OF THE DETERGENT N-HEPTYL-BETA-D-THIOGLUCOSIDE AT 1.7 ANGSTROMS