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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE PROTEIN OF DEGV FAMILY COG1307 WITH UNKNOWN FUNCTION FROM RUMINOCOCCUS GNAVUS ATCC 29149
 
Authors :  R. Zhang, C. Hatzos, S. Clancy, A. Joachimiak, Midwest Center For St Genomics (Mcsg)
Date :  08 Sep 09  (Deposition) - 20 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Degv Family, Psi2, Mcsg, Protein Structure Initiative, Midwest Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, C. Hatzos, S. Clancy, A. Joachimiak
The Crystal Structure Of The Protein Of Degv Family Cog1307 With Unknown Function From Ruminococcus Gnavus Atcc 29149
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED EGV FAMILY PROTEIN COG1307
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: RUMGNA_03254
    Organism Scientific: RUMINOCOCCUS GNAVUS
    Organism Taxid: 411470
    Strain: ATCC 29149

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric Unit (4, 22)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2NA4Ligand/IonSODIUM ION
3PG62Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION
3PG61Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 9)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION
3PG61Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:47 , THR A:80 , SER A:81 , LEU A:108 , SER A:109 , ARG A:137 , PHE A:178 , ARG A:191 , GLY A:215 , ILE A:295 , HOH A:326BINDING SITE FOR RESIDUE PG6 A 299
2AC2SOFTWAREGLN A:130 , THR A:159 , PHE A:160 , HOH A:529 , HOH A:539BINDING SITE FOR RESIDUE PO4 A 300
3AC3SOFTWAREARG A:224BINDING SITE FOR RESIDUE NA A 301
4AC4SOFTWAREARG A:87BINDING SITE FOR RESIDUE NA A 303
5AC5SOFTWARELEU B:47 , THR B:80 , CYS B:82 , LEU B:108 , SER B:109 , ARG B:137 , PHE B:178 , ARG B:191 , GLY B:215 , ILE B:295 , HOH B:348BINDING SITE FOR RESIDUE PG6 B 299
6AC6SOFTWAREASN A:204 , HOH A:333 , LYS B:23 , CYS B:94 , ASP B:95 , ALA B:96 , HOH B:494BINDING SITE FOR RESIDUE PO4 B 300
7AC7SOFTWARECYS B:77BINDING SITE FOR RESIDUE NA B 301

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:169 -B:169

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3JR7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JR7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JR7)

(-) Exons   (0, 0)

(no "Exon" information available for 3JR7)

(-) 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:279
 aligned with A7B6P0_RUMGN | A7B6P0 from UniProtKB/TrEMBL  Length:332

    Alignment length:281
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331 
         A7B6P0_RUMGN    52 KDMSYKVIVDSCGEFTPEMKADGGFEHVALGIQIEDTQWTDDDSLKQEELLLKIAESTSCAKTSCPSPERYMESYHCDAERIYVVTLSAELSGSYNSAVLGKNLYEEEYGEKQIHVFNSRSASVGETLIALKVQQCEKAGMTFEEVVESVECYIEEQHTYFVLENLDTLRKNGRLTGIKSLVAGALNIKPIMGSTPQGTICQKEKARGMKKALVKMADCVAADVVNAGDKILAIAHCNCEERAKEVQRLLKERFAVKSSFIVDTSGISTVYANDGGIIVVV 332
               SCOP domains d3jr7a_ A: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhh.eeee..eeee..eeee.....hhhhhhhhhhhh....eee..hhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhheeeee...hhhhhhh........--.....eeeeeee.....eeeeeeeehhhhhhhhhhhhhhhhh.hhhh.eeeeee..hhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhh...eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jr7 A  18 KDmSYKVIVDSCGEFTPEmKADGGFEHVALGIQIEDTQWTDDDSLKQEELLLKIAESTSCAKTSCPSPERYmESYHCDAERIYVVTLSAELSGSYNSAVLGKNLYEEEYGEKQIHVFNSRSASVGETLIALKVQQCEKAGmTFEEVVESVECYIEEQHTYFVLENLDTLRKNGRLTGIKS--AGALNIKPImGSTPQGTICQKEKARGmKKALVKmADCVAADVVNAGDKILAIAHCNCEERAKEVQRLLKERFAVKSSFIVDTSGISTVYANDGGIIVVV 298
                              |     27        37        47        57        67        77        87 |      97       107       117       127       137       147       157|      167       177       187       197  |    207 |     217       227     | 237       247       257       267       277       287       297 
                              |              36-MSE                                               89-MSE                                                              158-MSE                                197  |      209-MSE          226-MSE  |                                                                 
                             20-MSE                                                                                                                                                                             200                              233-MSE                                                             


Chain B from PDB  Type:PROTEIN  Length:279
 aligned with A7B6P0_RUMGN | A7B6P0 from UniProtKB/TrEMBL  Length:332

    Alignment length:281
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331 
         A7B6P0_RUMGN    52 KDMSYKVIVDSCGEFTPEMKADGGFEHVALGIQIEDTQWTDDDSLKQEELLLKIAESTSCAKTSCPSPERYMESYHCDAERIYVVTLSAELSGSYNSAVLGKNLYEEEYGEKQIHVFNSRSASVGETLIALKVQQCEKAGMTFEEVVESVECYIEEQHTYFVLENLDTLRKNGRLTGIKSLVAGALNIKPIMGSTPQGTICQKEKARGMKKALVKMADCVAADVVNAGDKILAIAHCNCEERAKEVQRLLKERFAVKSSFIVDTSGISTVYANDGGIIVVV 332
               SCOP domains d3jr7b_ B: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------DegV-3jr7B01 B:87-298                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------DegV-3jr7B02 B:87-298                                                                                                                                                                                                Pfam domains (2)
         Sec.struct. author ....eeeeee.....hhhhhh...eeee..eeee..eeee.....hhhhhhhhhhhh....eee..hhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.eeee...hhhhhhh...........--..eeeeeee.....eeeeeeeehhhhhhhhhhhhhhhhh.hhhh.eeeeee..hhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhh...eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jr7 B  18 KDmSYKVIVDSCGEFTPEmKADGGFEHVALGIQIEDTQWTDDDSLKQEELLLKIAESTSCAKTSCPSPERYmESYHCDAERIYVVTLSAELSGSYNSAVLGKNLYEEEYGEKQIHVFNSRSASVGETLIALKVQQCEKAGmTFEEVVESVECYIEEQHTYFVLENLDTLRKNGRLTGIKSLVA--LNIKPImGSTPQGTICQKEKARGmKKALVKmADCVAADVVNAGDKILAIAHCNCEERAKEVQRLLKERFAVKSSFIVDTSGISTVYANDGGIIVVV 298
                              |     27        37        47        57        67        77        87 |      97       107       117       127       137       147       157|      167       177       187       197  |  | 207 |     217       227     | 237       247       257       267       277       287       297 
                             20-MSE          36-MSE                                               89-MSE                                                              158-MSE                                   200  |     |              226-MSE  |                                                                 
                                                                                                                                                                                                                   203     |                     233-MSE                                                             
                                                                                                                                                                                                                         209-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JR7)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: EDD (22)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A7B6P0_RUMGN | A7B6P0)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.

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