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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 :  2.35
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, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CSU4Mod. Amino AcidCYSTEINE-S-SULFONIC ACID
2EDO6Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CSU1Mod. Amino AcidCYSTEINE-S-SULFONIC ACID
2EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CSU1Mod. Amino AcidCYSTEINE-S-SULFONIC ACID
2EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1CSU1Mod. Amino AcidCYSTEINE-S-SULFONIC ACID
2EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CSU1Mod. Amino AcidCYSTEINE-S-SULFONIC ACID
2EDO-1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS Y:40 , ASP Y:70 , GLN Y:71 , HOH Y:646BINDING SITE FOR RESIDUE EDO Y 601
2AC2SOFTWAREPHE B:10 , THR B:61 , ASN B:63 , LYS B:90 , HOH B:624 , GLY Y:12BINDING SITE FOR RESIDUE EDO B 602
3AC3SOFTWAREGLY D:12 , HOH D:636 , PHE F:10 , ASN F:63 , LYS F:90BINDING SITE FOR RESIDUE EDO D 603
4AC4SOFTWARESER C:32 , GLN C:34 , PRO C:67 , ALA C:68 , GLU D:56 , CSU D:110 , HOH D:605 , HOH D:637BINDING SITE FOR RESIDUE EDO D 604
5AC5SOFTWAREASN Y:54 , PRO Y:55 , GLU Y:56 , HOH Y:618 , HOH Y:629 , PRO Z:67 , ALA Z:68 , HOH Z:541BINDING SITE FOR RESIDUE EDO Y 605
6AC6SOFTWAREGLN A:34 , ALA A:68BINDING SITE FOR RESIDUE EDO A 606

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OXH)

(-) 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:107
 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 d2oxha_ A: 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
                 2oxh A   1 ADDAKPRVKVPSSAKAGETVTVKALISHKMESGQRKDADGKLIPRSIINRFTCELNGVNVVDVAIDPAVSTNPYFEFDAKVDAAGEFKFTWYDDDGSVYEDVKPIAV 107
                                    10        20        30        40        50        60        70        80        90       100       


Chain B from PDB  Type:PROTEIN  Length:115
 aligned with Q9LCU9_PARDE | Q9LCU9 from UniProtKB/TrEMBL  Length:140

    Alignment length:128
                                    22        32        42        52        62        72        82        92       102       112       122       132        
         Q9LCU9_PARDE    13 FGGLAAAALPGKAVMASTVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGGCGG 140
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-------------..hhhhhhhhhhh....ee...eee...ee.....eeeeee...eeeeeeee......eeeeeee.......eeeeee.....eeeeeeeee....eeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oxh B  -2 HG-------------SSTVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGGcGG 112
                             |       -     |   4        14        24        34        44        54        64        74        84        94       104     |  
                            -1             0                                                                                                           110-CSU


Chain C from PDB  Type:PROTEIN  Length:107
 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 d2oxhc_ 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
                 2oxh C   1 ADDAKPRVKVPSSAKAGETVTVKALISHKMESGQRKDADGKLIPRSIINRFTCELNGVNVVDVAIDPAVSTNPYFEFDAKVDAAGEFKFTWYDDDGSVYEDVKPIAV 107
                                    10        20        30        40        50        60        70        80        90       100       


Chain D 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...eeee...eeeeee.....eeeeee......eeeeeee...eeeeeeeeee.....eeeeeeee.....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2oxh D   1 STVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGGc 110
                                    10        20        30        40        50        60        70        80        90       100       110
                                                                                                                                       110-CSU


Chain E from PDB  Type:PROTEIN  Length:107
 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 d2oxhe_ E: 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
                 2oxh E   1 ADDAKPRVKVPSSAKAGETVTVKALISHKMESGQRKDADGKLIPRSIINRFTCELNGVNVVDVAIDPAVSTNPYFEFDAKVDAAGEFKFTWYDDDGSVYEDVKPIAV 107
                                    10        20        30        40        50        60        70        80        90       100       


Chain F from PDB  Type:PROTEIN  Length:114
 aligned with Q9LCU9_PARDE | Q9LCU9 from UniProtKB/TrEMBL  Length:140

    Alignment length:126
                                    24        34        44        54        64        74        84        94       104       114       124       134      
         Q9LCU9_PARDE    15 GLAAAALPGKAVMASTVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGGCGG 140
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .------------..hhhhhhhhhhh....ee...eee...ee.....eeeeee...eeeeeeee......eeeeeee.......eeeeee.....eeeeeeeee....eeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2oxh F  -1 G------------SSTVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGGcGG 112
                            |        -   |     6        16        26        36        46        56        66        76        86        96       106   |  
                            |            0                                                                                                           110-CSU
                           -1                                                                                                                             


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

    Alignment length:111
                                    37        47        57        67        77        87        97       107       117       127       137 
         Q9LCU9_PARDE    28 ASTVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGGC 138
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----SoxY-2oxhY01 Y:5-110                                                                                       Pfam domains (1)
           Pfam domains (2) -----SoxY-2oxhY02 Y:5-110                                                                                       Pfam domains (2)
           Pfam domains (3) -----SoxY-2oxhY03 Y:5-110                                                                                       Pfam domains (3)
           Pfam domains (4) -----SoxY-2oxhY04 Y:5-110                                                                                       Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhh.........eee...eeee...eeeeee.....eeeeee......eeeeeee...eeeeeeeeee.....eeeeeeee.....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2oxh Y   0 SSTVDELTAAFTGGAATGEGGLTLTAPEIAENGNTVPIEVKAPGAVAIMLLAAGNPEPAVATFNFGPAAADQRAATRIRLAQTQDVIALAKMADGSVVKAQTTVKVTIGGc 110
                                     9        19        29        39        49        59        69        79        89        99       109|
                                                                                                                                        110-CSU


Chain Z from PDB  Type:PROTEIN  Length:107
 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 d2oxhz_ Z: automated matches                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----SoxZ-2oxhZ01 Z:6-105                                                                                -- Pfam domains (1)
           Pfam domains (2) -----SoxZ-2oxhZ02 Z:6-105                                                                                -- Pfam domains (2)
           Pfam domains (3) -----SoxZ-2oxhZ03 Z:6-105                                                                                -- Pfam domains (3)
           Pfam domains (4) -----SoxZ-2oxhZ04 Z:6-105                                                                                -- Pfam domains (4)
         Sec.struct. author .....eeee.........eeeeeeee.....................eeeeeeee..eeeeeeee........eeeeeee....eeeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2oxh Z   1 ADDAKPRVKVPSSAKAGETVTVKALISHKMESGQRKDADGKLIPRSIINRFTCELNGVNVVDVAIDPAVSTNPYFEFDAKVDAAGEFKFTWYDDDGSVYEDVKPIAV 107
                                    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 2OXH)

(-) 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 2OXH)

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  2oxh
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 Related Entries

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

UniProtKB/TrEMBL
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(-) Related Entries Specified in the PDB File

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