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(-) Description

Title :  CRYSTAL STRUCTURE OF THE YGDR PROTEIN FROM E.COLI. NORTHEAST STRUCTURAL GENOMICS TARGET ER382A.
 
Authors :  A. P. Kuzin, M. Su, J. Seetharaman, P. Rossi, C. X. Chen, M. Jiang, K. Cunn L. Ma, R. Xiao, J. C. Liu, M. Baran, G. V. T. Swapna, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomic Consortium (Nesg)
Date :  11 Dec 08  (Deposition) - 06 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,Y
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  G  (1x)
Biol. Unit 8:  H  (1x)
Biol. Unit 9:  Y  (1x)
Keywords :  Ygdr Ygdr_ecoli Nesg X-Ray Structure, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Cell Membrane, Lipoprotein, Membrane, Palmitate, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. P. Kuzin, M. Su, J. Seetharaman, P. Rossi, C. X. Chen, M. Jiang, K. Cunningham, L. Ma, R. Xiao, J. C. Liu, M. Baran, G. V. T. Swapna, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of The Ygdr Protein From E. Coli. Northeas Structural Genomics Target Er382A.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED LIPOPROTEIN YGDR
    ChainsA, B, C, D, E, F, G, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3) + MAGIC
    Expression System Taxid562
    GeneYGDR, B2833, JW2801
    Organism ScientificESCHERICHIA COLI K-12
    Organism Taxid83333
 
Molecule 2 - UNCHARACTERIZED LIGAND
    ChainsY
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit ABCDEFGHY
Biological Unit 1 (1x)A        
Biological Unit 2 (1x) B       
Biological Unit 3 (1x)  C      
Biological Unit 4 (1x)   D     
Biological Unit 5 (1x)    E    
Biological Unit 6 (1x)     F   
Biological Unit 7 (1x)      G  
Biological Unit 8 (1x)       H 
Biological Unit 9 (1x)        Y

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 24)

Asymmetric Unit (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 6 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 7 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 8 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 9 (0, 0)
No.NameCountTypeFull Name
1MSE-1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3FIF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FIF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FIF)

(-) 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:55
 aligned with YGDR_ECOLI | P65294 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:55
                                                                             72    
                                    31        41        51        61        71|    
            YGDR_ECOLI   22 SDYVMATKDGRMILTDGKPEIDDDTGLVSYHDQQGNAMQINRDDVSQIIER----  -
               SCOP domains d3fifa_ A: automated matches                            SCOP domains
               CATH domains 3fifA00 A:3-57  [code=2.30.30.100, no name defined]     CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eee.....eee....eeeee.....eeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  3fif A  3 SDYVmATKDGRmILTDGKPEIDDDTGLVSYHDQQGNAmQINRDDVSQIIERLEHH 57
                                |   12 |      22        32       |42        52     
                                |     14-MSE                    40-MSE             
                                7-MSE                                              

Chain B from PDB  Type:PROTEIN  Length:56
 aligned with YGDR_ECOLI | P65294 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:56
                                                                              72    
                                    30        40        50        60        70 |    
            YGDR_ECOLI   21 SSDYVMATKDGRMILTDGKPEIDDDTGLVSYHDQQGNAMQINRDDVSQIIER----  -
               SCOP domains d3fifb_ B: automated matches                             SCOP domains
               CATH domains 3fifB00 B:2-57  [code=2.30.30.100, no name defined]      CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eee.....eee....eeeee.....eeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  3fif B  2 SSDYVmATKDGRmILTDGKPEIDDDTGLVSYHDQQGNAmQINRDDVSQIIERLEHH 57
                                 |  11  |     21        31        41        51      
                                 7-MSE 14-MSE                    40-MSE             

Chain C from PDB  Type:PROTEIN  Length:57
 aligned with YGDR_ECOLI | P65294 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:57
                                                                              72     
                                    30        40        50        60        70 |     
            YGDR_ECOLI   21 SSDYVMATKDGRMILTDGKPEIDDDTGLVSYHDQQGNAMQINRDDVSQIIER-----  -
               SCOP domains d3fifc_ C: automated matches                              SCOP domains
               CATH domains 3fifC00 C:2-58  [code=2.30.30.100, no name defined]       CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....ee.eeeeee.....eeeee.....eeeee...eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  3fif C  2 SSDYVmATKDGRmILTDGKPEIDDDTGLVSYHDQQGNAmQINRDDVSQIIERLEHHH 58
                                 |  11  |     21        31        41        51       
                                 7-MSE 14-MSE                    40-MSE              

Chain D from PDB  Type:PROTEIN  Length:57
 aligned with YGDR_ECOLI | P65294 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:57
                                                                              72     
                                    30        40        50        60        70 |     
            YGDR_ECOLI   21 SSDYVMATKDGRMILTDGKPEIDDDTGLVSYHDQQGNAMQINRDDVSQIIER-----  -
               SCOP domains d3fifd_ D: automated matches                              SCOP domains
               CATH domains 3fifD00 D:2-58  [code=2.30.30.100, no name defined]       CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eee.....ee.....eeeee.....eeeee...eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  3fif D  2 SSDYVmATKDGRmILTDGKPEIDDDTGLVSYHDQQGNAmQINRDDVSQIIERLEHHH 58
                                 |  11  |     21        31        41        51       
                                 7-MSE 14-MSE                    40-MSE              

Chain E from PDB  Type:PROTEIN  Length:52
 aligned with YGDR_ECOLI | P65294 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:56
                                                                              72    
                                    30        40        50        60        70 |    
            YGDR_ECOLI   21 SSDYVMATKDGRMILTDGKPEIDDDTGLVSYHDQQGNAMQINRDDVSQIIER----  -
               SCOP domains d3fife_ E: automated matches                             SCOP domains
               CATH domains 3fifE00 E:2-57  [code=2.30.30.100    , no name defined]  CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeee....ee.....eeee..----.eeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  3fif E  2 SSDYVmATKDGRmILTDGKPEIDDDTGLVSYHD----AmQINRDDVSQIIERLEHH 57
                                 |  11  |     21        31  |    |41        51      
                                 7-MSE 14-MSE              34   39|                 
                                                                 40-MSE             

Chain F from PDB  Type:PROTEIN  Length:56
 aligned with YGDR_ECOLI | P65294 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:56
                                                                              72    
                                    30        40        50        60        70 |    
            YGDR_ECOLI   21 SSDYVMATKDGRMILTDGKPEIDDDTGLVSYHDQQGNAMQINRDDVSQIIER----  -
               SCOP domains d3fiff_ F: automated matches                             SCOP domains
               CATH domains 3fifF00 F:2-57  [code=2.30.30.100, no name defined]      CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeee....eee....eeeee.....eeeee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  3fif F  2 SSDYVmATKDGRmILTDGKPEIDDDTGLVSYHDQQGNAmQINRDDVSQIIERLEHH 57
                                 |  11  |     21        31        41        51      
                                 7-MSE 14-MSE                    40-MSE             

Chain G from PDB  Type:PROTEIN  Length:57
 aligned with YGDR_ECOLI | P65294 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:57
                                                                              72     
                                    30        40        50        60        70 |     
            YGDR_ECOLI   21 SSDYVMATKDGRMILTDGKPEIDDDTGLVSYHDQQGNAMQINRDDVSQIIER-----  -
               SCOP domains d3fifg_ G: automated matches                              SCOP domains
               CATH domains 3fifG00 G:2-58  [code=2.30.30.100, no name defined]       CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeee....eee....eeeee.....eeeee...eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  3fif G  2 SSDYVmATKDGRmILTDGKPEIDDDTGLVSYHDQQGNAmQINRDDVSQIIERLEHHH 58
                                 |  11  |     21        31        41        51       
                                 7-MSE 14-MSE                    40-MSE              

Chain H from PDB  Type:PROTEIN  Length:55
 aligned with YGDR_ECOLI | P65294 from UniProtKB/Swiss-Prot  Length:72

    Alignment length:56
                                                                              72    
                                    30        40        50        60        70 |    
            YGDR_ECOLI   21 SSDYVMATKDGRMILTDGKPEIDDDTGLVSYHDQQGNAMQINRDDVSQIIER----  -
               SCOP domains d3fifh_ H: automated matches                             SCOP domains
               CATH domains 3fifH00 H:2-57  [code=2.30.30.100, n o name defined]     CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeee....eee....eeee.....-.eeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  3fif H  2 SSDYVmATKDGRmILTDGKPEIDDDTGLVSYHDQQG-AmQINRDDVSQIIERLEHH 57
                                 |  11  |     21        31     | |41        51      
                                 7-MSE 14-MSE                 37 ||                 
                                                                39|                 
                                                                 40-MSE             

Chain Y from PDB  Type:PROTEIN  Length:7
                                      
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                  3fif Y  1 GGGGGGG  7

   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 Unit

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (YGDR_ECOLI | P65294)
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        YGDR_ECOLI | P652942jn0

(-) Related Entries Specified in the PDB File

2jno THE SAME PROTEIN. RELATED ID: ER382A RELATED DB: TARGETDB