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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF FERREDOXIN:NADP+ REDUCTASE FROM MAIZE ROOT AT 1.05 ANGSTROMS
 
Authors :  H. R. Faber, P. A. Karplus
Date :  03 Feb 10  (Deposition) - 16 Mar 10  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Electron Transport, Oxidoreductase, Fad, Flavoprotein, Nadp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Tronrud, D. S. Berkholz, P. A. Karplus
Using A Conformation-Dependent Stereochemical Library Improves Crystallographic Refinement Of Proteins.
Acta Crystallogr. , Sect. D V. 66 834 2010
PubMed-ID: 20606264  |  Reference-DOI: 10.1107/S0907444910019207

(-) Compounds

Molecule 1 - FERREDOXIN--NADP REDUCTASE
    Chains: A
    EC Number: 1.18.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: MAIZE
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NA1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:91 , LEU A:92 , TYR A:93 , SER A:94 , CYS A:112 , VAL A:113 , ARG A:114 , ALA A:116 , TYR A:118 , LYS A:130 , ASN A:131 , GLY A:132 , VAL A:133 , CYS A:134 , SER A:135 , THR A:175 , LYS A:263 , GLU A:314 , TYR A:316 , HOH A:1067 , HOH A:1149 , HOH A:1189 , HOH A:1209 , HOH A:1257 , HOH A:1266 , HOH A:1310 , HOH A:1385 , HOH A:1411 , HOH A:1421 , HOH A:1533BINDING SITE FOR RESIDUE FAD A 415
2AC2SOFTWAREHOH A:1194 , HOH A:1316 , HOH A:1504 , HOH A:1510 , HOH A:1517 , HOH A:1549BINDING SITE FOR RESIDUE NA A 1800

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:139

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:13 -Pro A:14
2Gly A:151 -Pro A:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LO8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LO8)

(-) Exons   (0, 0)

(no "Exon" information available for 3LO8)

(-) 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:302
 aligned with Q41736_MAIZE | Q41736 from UniProtKB/TrEMBL  Length:327

    Alignment length:309
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318         
         Q41736_MAIZE    19 SKVSVAPLHLESAKEPPLNTYKPKEPFTATIVSVESLVGPKAPGETCHIVIDHGGNVPYWEGQSYGVIPPGENPKKPGAPQNVRLYSIASTRYGDNFDGRTGSLCVRRAVYYDPETGKEDPSKNGVCSNFLCNSKPGDKIQLTGPSGKIMLLPEEDPNATHIMIATGTGVAPFRGYLRRMFMEDVPNYRFGGLAWLFLGVANSDSLLYDEEFTSYLKQYPDNFRYDKALSREQKNRSGGKMYVQDKIEEYSDEIFKLLDGGAHIYFCGLKGMMPGIQDTLKKVAERRGESWDQKLAQLKKNKQWHVEVY 327
               SCOP domains d3lo8a1 A:8-156 automated matches                                                                                                                    d3lo8a2 A:157-316 automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------FAD_binding_6-3lo8A01 A:79-158                                                  -----------NAD_binding_1-3lo8A02 A:170-285                                                                                     ------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhhh..............eeeeeeeeee.........eeeeeee...........eeeee...............eeee.............eeeeeee............hhhhhhhhhhhhhh.....eeeeeeee.............eeeeeee...hhhhhhhhhhhhhee........eeeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee....-------.hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhh..eeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lo8 A   8 SKVSVAPLHLESAKEPPLNTYKPKEPFTATIVSVESLVGPKAPGETCHIVIDHGGNVPYWEGQSYGVIPPGENPKKPGAPQNVRLYSIASTRYGDNFDGRTGSLCVRRAVYYDPETGKEDPSKNGVCSNFLCNSKPGDKIQLTGPSGKIMLLPEEDPNATHIMIATGTGVAPFRGYLRRMFMEDVPNYRFGGLAWLFLGVANSDSLLYDEEFTSYLKQYPDNFRYDKALSREQ-------MYVQDKIEEYSDEIFKLLDGGAHIYFCGLKGMMPGIQDTLKKVAERRGESWDQKLAQLKKNKQWHVEVY 316
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237  |      -|      257       267       277       287       297       307         
                                                                                                                                                                                                                                                                  240     248
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LO8)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: FAD_Lum_binding (30)
(-)
Clan: NAD_Ferredoxin (30)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q41736_MAIZE | Q41736)
molecular function
    GO:0004324    ferredoxin-NADP+ reductase activity    Catalysis of the reaction: reduced ferredoxin + NADP+ = oxidized ferredoxin + NADPH + H+.
    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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  3lo8
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  1.18.1.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q41736_MAIZE | Q41736: 5h59 5h5j
UniProtKB/TrEMBL
        Q41736_MAIZE | Q41736: 1jb9 3lvb

(-) Related Entries Specified in the PDB File

1jb9 MODEL BASED ON DATA COLLECTED AT ROOM TEMPERATURE.