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(-) Description

Title :  THE SOXYZ COMPLEX OF PARACOCCUS PANTOTROPHUS
 
Authors :  V. Sauve, B. C. Berks, A. M. Hemmings
Date :  20 Feb 07  (Deposition) - 22 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B,C,D,E,F,Y,Z
Biol. Unit 1:  Y,Z  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  E,F  (1x)
Keywords :  Immunoglobulin-Like Beta-Sandwich Fold, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Sauve, S. Bruno, B. C. Berks, A. M. Hemmings
The Soxyz Complex Carries Sulfur Cycle Intermediates On A Peptide Swinging Arm.
J. Biol. Chem. V. 282 23194 2007
PubMed-ID: 17522046  |  Reference-DOI: 10.1074/JBC.M701602200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SOXZ PROTEIN
    Chains: Z, A, C, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PVS005
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: SOXZ
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 266
    Strain: LMD82.5T
 
Molecule 2 - SOXY PROTEIN
    Chains: Y, B, D, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PVS005
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: SOXY
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 266
    Strain: LMD82.5T

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFYZ
Biological Unit 1 (1x):       YZ
Biological Unit 2 (1x): AB      
Biological Unit 3 (1x):   CD    
Biological Unit 4 (1x):     EF  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY D:200 , HOH D:826 , THR Y:2BINDING SITE FOR RESIDUE SO4 D 801
2AC2SOFTWARELYS A:9 , ARG Z:50BINDING SITE FOR RESIDUE SO4 Z 802
3AC3SOFTWAREARG A:7 , LYS A:9 , LYS A:23 , TYR A:74 , HOH A:903 , HOH B:867BINDING SITE FOR RESIDUE SO4 A 803
4AC4SOFTWARETHR F:2 , VAL F:3 , ASP F:4 , HOH F:816 , HOH F:834 , HOH F:882BINDING SITE FOR RESIDUE EDO F 804
5AC5SOFTWAREASN Y:54 , PRO Y:55 , GLU Y:56 , CYS Y:110 , HOH Y:833 , PRO Z:67BINDING SITE FOR RESIDUE EDO Y 805
6AC6SOFTWAREASN B:54 , PRO B:55 , GLU B:56 , CYS B:110BINDING SITE FOR RESIDUE EDO B 806
7AC7SOFTWARESER A:32 , ARG A:45 , HOH A:864 , GLU B:56 , HOH B:813 , SER F:202BINDING SITE FOR RESIDUE EDO B 807

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OXG)

(-) 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:108
 aligned with Q9LCU8_PARDE | Q9LCU8 from UniProtKB/TrEMBL  Length:109

    Alignment length:108
                                    11        21        31        41        51        61        71        81        91       101        
         Q9LCU8_PARDE     2 ADDAKPRVKVPSSAKAGETVTVKALISHKMESGQRKDADGKLIPRSIINRFTCELNGVNVVDVAIDPAVSTNPYFEFDAKVDAAGEFKFTWYDDDGSVYEDVKPIAVA 109
               SCOP domains d2oxga_ A: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee........eeeeeeeee.....................eeeeeeee..eeeeeeee........eeeeeeee...eeeeeeeee....eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2oxg A   1 ADDAKPRVKVPSSAKAGETVTVKALISHKMESGQRKDADGKLIPRSIINRFTCELNGVNVVDVAIDPAVSTNPYFEFDAKVDAAGEFKFTWYDDDGSVYEDVKPIAVA 108
                                    10        20        30        40        50        60        70        80        90       100        


Chain B from PDB  Type:PROTEIN  Length:110
 aligned with Q9LCU9_PARDE | Q9LCU9 from UniProtKB/TrEMBL  Length:140

    Alignment length:110
                                    38        48        58        68        78        88        98       108       118       128       138
         Q9LCU9_PARDE    29 STVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGGC 138
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.........eee...ee.....eeeeee.....eeeeee......eeeeeee.......eeeeee.....eeeeeeee.....eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2oxg B   1 STVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGGC 110
                                    10        20        30        40        50        60        70        80        90       100       110


Chain C from PDB  Type:PROTEIN  Length:101
 aligned with Q9LCU8_PARDE | Q9LCU8 from UniProtKB/TrEMBL  Length:109

    Alignment length:107
                                    11        21        31        41        51        61        71        81        91       101       
         Q9LCU8_PARDE     2 ADDAKPRVKVPSSAKAGETVTVKALISHKMESGQRKDADGKLIPRSIINRFTCELNGVNVVDVAIDPAVSTNPYFEFDAKVDAAGEFKFTWYDDDGSVYEDVKPIAV 108
               SCOP domains d2oxgc_ C: automated matches                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee........eeeeeeeee..........------.....eeeeeeee..eeeeeeee........eeeeeeee...eeeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2oxg C   1 ADDAKPRVKVPSSAKAGETVTVKALISHKMESGQRK------IPRSIINRFTCELNGVNVVDVAIDPAVSTNPYFEFDAKVDAAGEFKFTWYDDDGSVYEDVKPIAV 107
                                    10        20        30     |   -  |     50        60        70        80        90       100       
                                                              36     43                                                                


Chain D from PDB  Type:PROTEIN  Length:111
 aligned with Q9LCU9_PARDE | Q9LCU9 from UniProtKB/TrEMBL  Length:140

    Alignment length:115
                                    32        42        52        62        72        82        92       102       112       122       132     
         Q9LCU9_PARDE    23 GKAVMASTVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGG 137
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----.hhhhhhhhhh..........eee...eeee...eeeeee...eeeeeeee......eeeeeee...eeeeeeeeee.....eeeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2oxg D 200 GS----STVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGG 109
                             |    |  4        14        24        34        44        54        64        74        84        94       104     
                           201    1                                                                                                            


Chain E from PDB  Type:PROTEIN  Length:99
 aligned with Q9LCU8_PARDE | Q9LCU8 from UniProtKB/TrEMBL  Length:109

    Alignment length:106
                                    13        23        33        43        53        63        73        83        93       103      
         Q9LCU8_PARDE     4 DAKPRVKVPSSAKAGETVTVKALISHKMESGQRKDADGKLIPRSIINRFTCELNGVNVVDVAIDPAVSTNPYFEFDAKVDAAGEFKFTWYDDDGSVYEDVKPIAVA 109
               SCOP domains d2oxge_ E: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee........eeeeeeee.........-------......eeeeeeee..eeeeeeee........eeeeeeee...eeeeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2oxg E   3 DAKPRVKVPSSAKAGETVTVKALISHKMESGQ-------LIPRSIINRFTCELNGVNVVDVAIDPAVSTNPYFEFDAKVDAAGEFKFTWYDDDGSVYEDVKPIAVA 108
                                    12        22        32 |      42        52        62        72        82        92       102      
                                                          34      42                                                                  


Chain F from PDB  Type:PROTEIN  Length:112
 aligned with Q9LCU9_PARDE | Q9LCU9 from UniProtKB/TrEMBL  Length:140

    Alignment length:125
                                    22        32        42        52        62        72        82        92       102       112       122       132     
         Q9LCU9_PARDE    13 FGGLAAAALPGKAVMASTVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGG 137
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-------------.hhhhhhhhhhh....ee...eee...eeee...eeeeee.....eeeeee......eeeeeee...eeeeeeeeee.....eeeeeeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oxg F 200 HGS-------------STVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGG 109
                              |      -      |  4        14        24        34        44        54        64        74        84        94       104     
                            202             1                                                                                                            


Chain Y from PDB  Type:PROTEIN  Length:112
 aligned with Q9LCU9_PARDE | Q9LCU9 from UniProtKB/TrEMBL  Length:140

    Alignment length:116
                                    32        42        52        62        72        82        92       102       112       122       132      
         Q9LCU9_PARDE    23 GKAVMASTVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGGC 138
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------SoxY-2oxgY01 Y:5-110                                                                                       Pfam domains (1)
           Pfam domains (2) ----------SoxY-2oxgY02 Y:5-110                                                                                       Pfam domains (2)
           Pfam domains (3) ----------SoxY-2oxgY03 Y:5-110                                                                                       Pfam domains (3)
           Pfam domains (4) ----------SoxY-2oxgY04 Y:5-110                                                                                       Pfam domains (4)
         Sec.struct. author ..----hhhhhhhhhhhh...ee....eee...eeee...eeeeee...eeeeeeee......eeeeeee...eeeeeeeeee.....eeeeeeeee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2oxg Y 200 GS----STVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGGC 110
                             |    |  4        14        24        34        44        54        64        74        84        94       104      
                           201    1                                                                                                             


Chain Z from PDB  Type:PROTEIN  Length:108
 aligned with Q9LCU8_PARDE | Q9LCU8 from UniProtKB/TrEMBL  Length:109

    Alignment length:108
                                    11        21        31        41        51        61        71        81        91       101        
         Q9LCU8_PARDE     2 ADDAKPRVKVPSSAKAGETVTVKALISHKMESGQRKDADGKLIPRSIINRFTCELNGVNVVDVAIDPAVSTNPYFEFDAKVDAAGEFKFTWYDDDGSVYEDVKPIAVA 109
               SCOP domains d2oxgz_ Z: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----SoxZ-2oxgZ01 Z:6-105                                                                                --- Pfam domains (1)
           Pfam domains (2) -----SoxZ-2oxgZ02 Z:6-105                                                                                --- Pfam domains (2)
           Pfam domains (3) -----SoxZ-2oxgZ03 Z:6-105                                                                                --- Pfam domains (3)
           Pfam domains (4) -----SoxZ-2oxgZ04 Z:6-105                                                                                --- Pfam domains (4)
         Sec.struct. author .....eeee...ee...eeeeeeeee.....................eeeeeeee..eeeeeeee........eeeeeeee...eeeeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2oxg Z   1 ADDAKPRVKVPSSAKAGETVTVKALISHKMESGQRKDADGKLIPRSIINRFTCELNGVNVVDVAIDPAVSTNPYFEFDAKVDAAGEFKFTWYDDDGSVYEDVKPIAVA 108
                                    10        20        30        40        50        60        70        80        90       100
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OXG)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: E-set (290)
(-)
Clan: SOR (12)

(-) Gene Ontology  (0, 0)

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

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  2oxg
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 Related Entries

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

UniProtKB/TrEMBL
        Q9LCU8_PARDE | Q9LCU8: 2ox5 2oxh
        Q9LCU9_PARDE | Q9LCU9: 2ox5 2oxh

(-) Related Entries Specified in the PDB File

2ox5 THE CARRIER CYSTEINE RESIDUE OF SOXY IS MODIFIED BY ADDITION OF BETA-MERCAPTOETHANOL