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(-) Description

Title :  CRYSTAL STRUCTURE OF A DIMERIC FERREDOXIN-LIKE PROTEIN (JCVI_PEP_1096682647733) FROM UNCULTURED MARINE ORGANISM AT 1.85 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  21 Dec 06  (Deposition) - 23 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Metagenomics Target, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Jcvi_pep_1096682647733) From An Environmental Metagenome (Unidentified Marine Microbe), Sorcerer Ii Global Ocean Sampling Experiment At 1. 85 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: UNCULTURED MARINE ORGANISM
    Organism Taxid: 360281
    Other Details: SYNTHETIC GENE: THE GENE PRODUCT WAS BASED ON JCVI_PEP_1096682647733 FROM THE SORCERER II GLOBAL OCEAN SAMPLING EXPERIMENT

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 36)

Asymmetric Unit (3, 36)
No.NameCountTypeFull Name
1EDO11Ligand/Ion1,2-ETHANEDIOL
2MSE21Mod. Amino AcidSELENOMETHIONINE
3OHA4Ligand/Ion10-OXOHEXADECANOIC ACID
Biological Unit 1 (3, 17)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MSE11Mod. Amino AcidSELENOMETHIONINE
3OHA2Ligand/Ion10-OXOHEXADECANOIC ACID
Biological Unit 2 (3, 19)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2MSE10Mod. Amino AcidSELENOMETHIONINE
3OHA2Ligand/Ion10-OXOHEXADECANOIC ACID

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:8 , THR A:10 , TYR A:64 , TYR A:66 , ILE A:76 , ARG A:102BINDING SITE FOR RESIDUE OHA A 300
02AC2SOFTWARESER B:8 , THR B:10 , VAL B:27 , THR B:30 , TYR B:64 , TYR B:66 , ILE B:76 , LEU B:79 , PHE B:83 , PHE B:89 , THR B:100 , ARG B:102BINDING SITE FOR RESIDUE OHA B 300
03AC3SOFTWARESER C:8 , THR C:10 , THR C:30 , TYR C:64 , TYR C:66 , ILE C:76 , PHE C:83 , THR C:100 , ARG C:102BINDING SITE FOR RESIDUE OHA C 300
04AC4SOFTWARESER D:8 , THR D:10 , VAL D:27 , THR D:30 , TYR D:64 , TYR D:66 , PHE D:72 , LEU D:79 , PHE D:83 , PHE D:89 , LEU D:92 , THR D:100 , ARG D:102 , HOH D:346BINDING SITE FOR RESIDUE OHA D 300
05AC5SOFTWAREHOH A:309 , ARG D:41 , ALA D:74 , ALA D:77 , HOH D:378BINDING SITE FOR RESIDUE EDO D 301
06AC6SOFTWARELYS C:54 , THR D:99 , THR D:100 , SER D:101 , HOH D:306BINDING SITE FOR RESIDUE EDO D 302
07AC7SOFTWAREVAL C:106 , GLU D:21 , ILE D:24 , ARG D:50BINDING SITE FOR RESIDUE EDO D 303
08AC8SOFTWAREARG A:69 , GLU A:73 , HOH A:372BINDING SITE FOR RESIDUE EDO A 301
09AC9SOFTWAREGLU B:21 , ILE B:24 , ARG B:50BINDING SITE FOR RESIDUE EDO B 301
10BC1SOFTWARELYS C:5 , ILE C:15 , GLU C:65 , GLU C:108 , HOH C:349 , LYS D:45BINDING SITE FOR RESIDUE EDO C 301
11BC2SOFTWAREARG A:50 , VAL A:51 , TRP A:52 , GLY A:55 , HOH A:324 , HOH A:359 , ARG D:41 , ALA D:74BINDING SITE FOR RESIDUE EDO D 304
12BC3SOFTWAREVAL B:33 , GLU B:37 , TYR B:78 , HOH B:390 , PRO D:87BINDING SITE FOR RESIDUE EDO B 302
13BC4SOFTWAREPHE C:9 , HOH C:317 , HOH D:306 , HOH D:312BINDING SITE FOR RESIDUE EDO C 303
14BC5SOFTWAREPHE A:9 , HOH A:312 , PHE B:9 , HOH B:348 , HOH B:367 , HOH B:368BINDING SITE FOR RESIDUE EDO B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OD6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OD6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OD6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OD6)

(-) Exons   (0, 0)

(no "Exon" information available for 2OD6)

(-) 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:110
                                                                                                                                              
               SCOP domains -d2od6a1 A:1-109 Hypothetical protein GOS_2359375                                                              SCOP domains
               CATH domains 2od6A00 A:0-109  [code=3.30.70.900, no name defined]                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhh....hhhhhh...eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2od6 A   0 GmAEPKFTSFTTADFINDVDmELFIDAVEKTAPVWVKEmKSRGLLKFSmNRVWNKGEVFRVVmTYEYKDRASFEANIAYLEDTFGKNPVFLQLVTTAKFTTSRCLVVmEV 109
                             |       9        19|       29        39        49        59  |     69        79        89        99       109
                             |                 20-MSE            38-MSE    48-MSE        62-MSE                                      107-MSE
                             1-MSE                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d2od6b1 B:2-109 Hypothetical protein GOS_2359375                                                             SCOP domains
               CATH domains 2od6B00 B:2-109  [code=3.30.70.900, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhh...eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2od6 B   2 AEPKFTSFTTADFINDVDmELFIDAVEKTAPVWVKEmKSRGLLKFSmNRVWNKGEVFRVVmTYEYKDRASFEANIAYLEDTFGKNPVFLQLVTTAKFTTSRCLVVmEV 109
                                    11        21        31      | 41      | 51        61|       71        81        91       101     |  
                                             20-MSE            38-MSE    48-MSE        62-MSE                                      107-MSE


Chain C from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains d2od6c1 C:3-109 Hypothetical protein GOS_2359375                                                            SCOP domains
               CATH domains 2od6C00 C:3-109  [code=3.30.70.900, no name defined]                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhh.hhhhhhhh...eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2od6 C   3 EPKFTSFTTADFINDVDmELFIDAVEKTAPVWVKEmKSRGLLKFSmNRVWNKGEVFRVVmTYEYKDRASFEANIAYLEDTFGKNPVFLQLVTTAKFTTSRCLVVmEV 109
                                    12       |22        32     |  42     |  52        62        72        82        92       102    |  
                                            20-MSE            38-MSE    48-MSE        62-MSE                                      107-MSE


Chain D from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d2od6d1 D:2-109 Hypothetical protein GOS_2359375                                                             SCOP domains
               CATH domains 2od6D00 D:2-109  [code=3.30.70.900, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhh...eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2od6 D   2 AEPKFTSFTTADFINDVDmELFIDAVEKTAPVWVKEmKSRGLLKFSmNRVWNKGEVFRVVmTYEYKDRASFEANIAYLEDTFGKNPVFLQLVTTAKFTTSRCLVVmEV 109
                                    11        21        31      | 41      | 51        61|       71        81        91       101     |  
                                             20-MSE            38-MSE    48-MSE        62-MSE                                      107-MSE
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OD6)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2OD6)

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