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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE THIOL:DISULFIDE INTERCHANGE PROTEIN DSBE FROM CHLOROBIUM TEPIDUM
 
Authors :  L. Damodharan, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  11 Mar 09  (Deposition) - 31 Mar 09  (Release) - 31 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  C  (1x)
Biol. Unit 5:  D  (1x)
Keywords :  Oxidoreductase, Psi-Ii, 11210H, Thiol:Disulfide Interchange Protein Dsbe, Putative, Chlorobium Tepidum, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, New York Structural Genomix Research Consortium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Damodharan, S. K. Burley, S. Swaminathan
Crystal Structure Of A Putative Thiol:Disulfide Interchange Protein Dsbe From Chlorobium Tepidum
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1
    Atcc: 49652
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGX3(BC)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 30-170
    Gene: CT1072
    Organism Scientific: CHLOROBIUM TEPIDUM TLS
    Organism Taxid: 194439
    Strain: TLS / DSM 12025

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): A   
Biological Unit 3 (1x):  B  
Biological Unit 4 (1x):   C 
Biological Unit 5 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3GL3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GL3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Mse A:132 -Pro A:133
2Mse B:132 -Pro B:133
3Mse C:132 -Pro C:133
4Mse D:132 -Pro D:133

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GL3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GL3)

(-) Exons   (0, 0)

(no "Exon" information available for 3GL3)

(-) 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:141
 aligned with Q8KDH8_CHLTE | Q8KDH8 from UniProtKB/TrEMBL  Length:170

    Alignment length:141
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167 
         Q8KDH8_CHLTE    28 ALDKGDKAPDFALPGKTGVVKLSDKTGSVVYLDFWASWCGPCRQSFPWMNQMQAKYKAKGFQVVAVNLDAKTGDAMKFLAQVPAEFTVAFDPKGQTPRLYGVKGMPTSFLIDRNGKVLLQHVGFRPADKEALEQQILAALG 168
               SCOP domains d3gl3a_ A: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee....eee.hhhh..eeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhh....eeee...hhhhhhh......eeeee.....eeeeee.....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gl3 A  28 SLDKGDKAPDFALPGKTGVVKLSDKTGSVVYLDFWASWCGPCRQSFPWmNQmQAKYKAKGFQVVAVNLDAKTGDAmKFLAQVPAEFTVAFDPKGQTPRLYGVKGmPTSFLIDRNGKVLLQHVGFRPADKEALEQQILAALG 168
                                    37        47        57        67        77 |      87        97     | 107       117       127    |  137       147       157       167 
                                                                           76-MSE                    103-MSE                      132-MSE                                
                                                                              79-MSE                                                                                     


Chain B from PDB  Type:PROTEIN  Length:141
 aligned with Q8KDH8_CHLTE | Q8KDH8 from UniProtKB/TrEMBL  Length:170

    Alignment length:141
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168 
         Q8KDH8_CHLTE    29 LDKGDKAPDFALPGKTGVVKLSDKTGSVVYLDFWASWCGPCRQSFPWMNQMQAKYKAKGFQVVAVNLDAKTGDAMKFLAQVPAEFTVAFDPKGQTPRLYGVKGMPTSFLIDRNGKVLLQHVGFRPADKEALEQQILAALGG 169
               SCOP domains d3gl3b_ B: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee....eee.hhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhh....eeee....hhhhhh......eeeee.....eeeeee..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gl3 B  29 LDKGDKAPDFALPGKTGVVKLSDKTGSVVYLDFWASWCGPCRQSFPWmNQmQAKYKAKGFQVVAVNLDAKTGDAmKFLAQVPAEFTVAFDPKGQTPRLYGVKGmPTSFLIDRNGKVLLQHVGFRPADKEALEQQILAALGG 169
                                    38        48        58        68       |78|       88        98    |  108       118       128   |   138       148       158       168 
                                                                          76-MSE                    103-MSE                      132-MSE                                 
                                                                             79-MSE                                                                                      


Chain C from PDB  Type:PROTEIN  Length:138
 aligned with Q8KDH8_CHLTE | Q8KDH8 from UniProtKB/TrEMBL  Length:170

    Alignment length:138
                                    39        49        59        69        79        89        99       109       119       129       139       149       159        
         Q8KDH8_CHLTE    30 DKGDKAPDFALPGKTGVVKLSDKTGSVVYLDFWASWCGPCRQSFPWMNQMQAKYKAKGFQVVAVNLDAKTGDAMKFLAQVPAEFTVAFDPKGQTPRLYGVKGMPTSFLIDRNGKVLLQHVGFRPADKEALEQQILAAL 167
               SCOP domains d3gl3c_ C: automated matches                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eee....eee.hhhh..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhh....eeee...hhhhhhh......eeeee.....eeeeee....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gl3 C  30 DKGDKAPDFALPGKTGVVKLSDKTGSVVYLDFWASWCGPCRQSFPWmNQmQAKYKAKGFQVVAVNLDAKTGDAmKFLAQVPAEFTVAFDPKGQTPRLYGVKGmPTSFLIDRNGKVLLQHVGFRPADKEALEQQILAAL 167
                                    39        49        59        69      | 79        89        99   |   109       119       129  |    139       149       159        
                                                                         76-MSE                    103-MSE                      132-MSE                               
                                                                            79-MSE                                                                                    


Chain D from PDB  Type:PROTEIN  Length:137
 aligned with Q8KDH8_CHLTE | Q8KDH8 from UniProtKB/TrEMBL  Length:170

    Alignment length:137
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q8KDH8_CHLTE    31 KGDKAPDFALPGKTGVVKLSDKTGSVVYLDFWASWCGPCRQSFPWMNQMQAKYKAKGFQVVAVNLDAKTGDAMKFLAQVPAEFTVAFDPKGQTPRLYGVKGMPTSFLIDRNGKVLLQHVGFRPADKEALEQQILAAL 167
               SCOP domains d3gl3d_ D: automated matches                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee....eee.hhhh..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhh......eeee...hhhhhhh......eeeee.......eeee.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gl3 D  31 KGDKAPDFALPGKTGVVKLSDKTGSVVYLDFWASWCGPCRQSFPWmNQmQAKYKAKGFQVVAVNLDAKTGDAmKFLAQVPAEFTVAFDPKGQTPRLYGVKGmPTSFLIDRNGKVLLQHVGFRPADKEALEQQILAAL 167
                                    40        50        60        70     |  80        90       100  |    110       120       130 |     140       150       160       
                                                                        76-MSE                    103-MSE                      132-MSE                               
                                                                           79-MSE
   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  (1, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GL3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GL3)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8KDH8_CHLTE | Q8KDH8)
molecular function
    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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