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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUTAREDOXIN-LIKE PROTEIN FROM AQUIFEX AEOLICUS
 
Authors :  A. Ebihara, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/P Initiative (Rsgi)
Date :  20 Apr 07  (Deposition) - 23 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Redox Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ebihara, S. Yokoyama, S. Kuramitsu
Crystal Structure Of Glutaredoxin-Like Protein From Aquifex Aeolicus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTAREDOXIN-LIKE PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL-X
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 16)

Asymmetric/Biological Unit (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2YWM)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:34 -A:37
2B:34 -B:37
3C:34 -C:37
4D:34 -D:37

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Val A:82 -Pro A:83
2Val A:190 -Pro A:191
3Val B:82 -Pro B:83
4Val B:190 -Pro B:191
5Val C:82 -Pro C:83
6Val C:190 -Pro C:191
7Val D:82 -Pro D:83
8Val D:190 -Pro D:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YWM)

(-) 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:228
 aligned with O66753_AQUAE | O66753 from UniProtKB/TrEMBL  Length:229

    Alignment length:228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        
         O66753_AQUAE     1 MLLNLDVRMQLKELAQKEFKEPVSIKLFSQAIGCESCQTAEELLKETVEVIGEAVGQDKIKLDIYSPFTHKEETEKYGVDRVPTIVIEGDKDYGIRYIGLPAGLEFTTLINGIFHVSQRKPQLSEKTLELLQVVDIPIEIWVFVTTSCGYCPSAAVMAWDFALANDYITSKVIDASENQDLAEQFQVVGVPKIVINKGVAEFVGAQPENAFLGYIMAVYEKLKREKEQ 228
               SCOP domains d2ywma1 A:1-121 automated matches                                                                                        d2ywma2 A:122-228 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------2ywmA02 A:117-225 Glutaredoxin                                                                               --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhh......eeeee......eeee.....hhhhhhhhhhhhhhh.....hhhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh......eeee....eeee...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ywm A   1 mLLNLDVRmQLKELAQKEFKEPVSIKLFSQAIGCESCQTAEELLKETVEVIGEAVGQDKIKLDIYSPFTHKEETEKYGVDRVPTIVIEGDKDYGIRYIGLPAGLEFTTLINGIFHVSQRKPQLSEKTLELLQVVDIPIEIWVFVTTSCGYCPSAAVmAWDFALANDYITSKVIDASENQDLAEQFQVVGVPKIVINKGVAEFVGAQPENAFLGYImAVYEKLKREKEQ 228
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |160       170       180       190       200       210     | 220        
                            |       9-MSE                                                                                                                                             157-MSE                                                    216-MSE        
                            1-MSE                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with O66753_AQUAE | O66753 from UniProtKB/TrEMBL  Length:229

    Alignment length:228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        
         O66753_AQUAE     1 MLLNLDVRMQLKELAQKEFKEPVSIKLFSQAIGCESCQTAEELLKETVEVIGEAVGQDKIKLDIYSPFTHKEETEKYGVDRVPTIVIEGDKDYGIRYIGLPAGLEFTTLINGIFHVSQRKPQLSEKTLELLQVVDIPIEIWVFVTTSCGYCPSAAVMAWDFALANDYITSKVIDASENQDLAEQFQVVGVPKIVINKGVAEFVGAQPENAFLGYIMAVYEKLKREKEQ 228
               SCOP domains d2ywmb1 B:1-121 automated matches                                                                                        d2ywmb2 B:122-228 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------2ywmB02 B:117-225 Glutaredoxin                                                                               --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhh......eeeee......eeee.....hhhhhhhhhhhhhhh.....hhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh......eeee....eeee...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ywm B   1 mLLNLDVRmQLKELAQKEFKEPVSIKLFSQAIGCESCQTAEELLKETVEVIGEAVGQDKIKLDIYSPFTHKEETEKYGVDRVPTIVIEGDKDYGIRYIGLPAGLEFTTLINGIFHVSQRKPQLSEKTLELLQVVDIPIEIWVFVTTSCGYCPSAAVmAWDFALANDYITSKVIDASENQDLAEQFQVVGVPKIVINKGVAEFVGAQPENAFLGYImAVYEKLKREKEQ 228
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |160       170       180       190       200       210     | 220        
                            1-MSE   9-MSE                                                                                                                                             157-MSE                                                    216-MSE        


Chain C from PDB  Type:PROTEIN  Length:228
 aligned with O66753_AQUAE | O66753 from UniProtKB/TrEMBL  Length:229

    Alignment length:228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        
         O66753_AQUAE     1 MLLNLDVRMQLKELAQKEFKEPVSIKLFSQAIGCESCQTAEELLKETVEVIGEAVGQDKIKLDIYSPFTHKEETEKYGVDRVPTIVIEGDKDYGIRYIGLPAGLEFTTLINGIFHVSQRKPQLSEKTLELLQVVDIPIEIWVFVTTSCGYCPSAAVMAWDFALANDYITSKVIDASENQDLAEQFQVVGVPKIVINKGVAEFVGAQPENAFLGYIMAVYEKLKREKEQ 228
               SCOP domains d2ywmc1 C:1-121 automated matches                                                                                        d2ywmc2 C:122-228 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------2ywmC02 C:117-225 Glutaredoxin                                                                               --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhh......eeeee......eeee.....hhhhhhhhhhhhhhh.....hhhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh......eeee....eeee...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ywm C   1 mLLNLDVRmQLKELAQKEFKEPVSIKLFSQAIGCESCQTAEELLKETVEVIGEAVGQDKIKLDIYSPFTHKEETEKYGVDRVPTIVIEGDKDYGIRYIGLPAGLEFTTLINGIFHVSQRKPQLSEKTLELLQVVDIPIEIWVFVTTSCGYCPSAAVmAWDFALANDYITSKVIDASENQDLAEQFQVVGVPKIVINKGVAEFVGAQPENAFLGYImAVYEKLKREKEQ 228
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |160       170       180       190       200       210     | 220        
                            1-MSE   9-MSE                                                                                                                                             157-MSE                                                    216-MSE        


Chain D from PDB  Type:PROTEIN  Length:227
 aligned with O66753_AQUAE | O66753 from UniProtKB/TrEMBL  Length:229

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
         O66753_AQUAE     1 MLLNLDVRMQLKELAQKEFKEPVSIKLFSQAIGCESCQTAEELLKETVEVIGEAVGQDKIKLDIYSPFTHKEETEKYGVDRVPTIVIEGDKDYGIRYIGLPAGLEFTTLINGIFHVSQRKPQLSEKTLELLQVVDIPIEIWVFVTTSCGYCPSAAVMAWDFALANDYITSKVIDASENQDLAEQFQVVGVPKIVINKGVAEFVGAQPENAFLGYIMAVYEKLKREKE 227
               SCOP domains d2ywmd1 D:1-121 automated matches                                                                                        d2ywmd2 D:122-227 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------2ywmD02 D:117-225 Glutaredoxin                                                                               -- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------Thioredoxin_3-2ywmD01 D:138-217                                                 ---------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------Thioredoxin_3-2ywmD02 D:138-217                                                 ---------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------Thioredoxin_3-2ywmD03 D:138-217                                                 ---------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------Thioredoxin_3-2ywmD04 D:138-217                                                 ---------- Pfam domains (4)
           Pfam domains (5) -----------------------------------------------------------------------------------------------------------------------------------------Thioredoxin_3-2ywmD05 D:138-217                                                 ---------- Pfam domains (5)
           Pfam domains (6) -----------------------------------------------------------------------------------------------------------------------------------------Thioredoxin_3-2ywmD06 D:138-217                                                 ---------- Pfam domains (6)
           Pfam domains (7) -----------------------------------------------------------------------------------------------------------------------------------------Thioredoxin_3-2ywmD07 D:138-217                                                 ---------- Pfam domains (7)
           Pfam domains (8) -----------------------------------------------------------------------------------------------------------------------------------------Thioredoxin_3-2ywmD08 D:138-217                                                 ---------- Pfam domains (8)
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhh......eeeee......eeee.....hhhhhhhhhhhhhhhh....hhhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh......eeee....eeee...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ywm D   1 mLLNLDVRmQLKELAQKEFKEPVSIKLFSQAIGCESCQTAEELLKETVEVIGEAVGQDKIKLDIYSPFTHKEETEKYGVDRVPTIVIEGDKDYGIRYIGLPAGLEFTTLINGIFHVSQRKPQLSEKTLELLQVVDIPIEIWVFVTTSCGYCPSAAVmAWDFALANDYITSKVIDASENQDLAEQFQVVGVPKIVINKGVAEFVGAQPENAFLGYImAVYEKLKREKE 227
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |160       170       180       190       200       210     | 220       
                            1-MSE   9-MSE                                                                                                                                             157-MSE                                                    216-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Fold: Thioredoxin fold (994)
(-)
Superfamily: Thioredoxin-like (992)
(-)
Family: automated matches (347)
(-)
Protein domain: automated matches (347)
(-)
Aquifex aeolicus [TaxId: 224324] (2)
1ad2ywma1A:1-121
1bd2ywmd1D:1-121
1cd2ywmd2D:122-227
1dd2ywma2A:122-228
1ed2ywmb1B:1-121
1fd2ywmb2B:122-228
1gd2ywmc1C:1-121
1hd2ywmc2C:122-228

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 8)

Asymmetric/Biological Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2YWM)

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Asymmetric/Biological Unit
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  Cis Peptide Bonds
    Val A:190 - Pro A:191   [ RasMol ]  
    Val A:82 - Pro A:83   [ RasMol ]  
    Val B:190 - Pro B:191   [ RasMol ]  
    Val B:82 - Pro B:83   [ RasMol ]  
    Val C:190 - Pro C:191   [ RasMol ]  
    Val C:82 - Pro C:83   [ RasMol ]  
    Val D:190 - Pro D:191   [ RasMol ]  
    Val D:82 - Pro D:83   [ RasMol ]  
 

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  2ywm
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 Related Entries

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

UniProtKB/TrEMBL
        O66753_AQUAE | O66753: 2ayt

(-) Related Entries Specified in the PDB File

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