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(-) Description

Title :  CRYSTAL STRUCTURE OF GENE PRODUCT SO3848 FROM SHEWANELLA ONEIDENSIS MR-1
 
Authors :  R. Zhang, L. Bigelow, S. Giuliani, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  19 Feb 07  (Deposition) - 03 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Shewanella Oneidensis, Structural Genomics, Psi-2, Mcsg, Protein Structure Initiative, Midwest Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, L. Bigelow, S. Giuliani, A. Joachimiak
The Crystal Structure Of Gene Product So3848 From Shewanell Oneidensis Mr-1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN SO3848
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: SO_3848
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 211586
    Strain: MR-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1MG10Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:32 , GLU A:36 , HOH A:249 , HOH A:349 , HOH A:376BINDING SITE FOR RESIDUE MG A 167
02AC2SOFTWAREASP A:57 , GLU D:140BINDING SITE FOR RESIDUE MG A 168
03AC3SOFTWAREGLU A:74 , GLU C:74 , HOH C:258BINDING SITE FOR RESIDUE MG C 167
04AC4SOFTWAREGLU B:74 , HOH B:177 , HOH B:358 , HIS C:84BINDING SITE FOR RESIDUE MG C 168
05AC5SOFTWAREGLU A:123 , HOH A:314BINDING SITE FOR RESIDUE MG A 169
06AC6SOFTWAREGLU B:123 , HOH B:352 , GLU C:129 , HOH C:252BINDING SITE FOR RESIDUE MG C 169
07AC7SOFTWAREASP B:71 , HOH B:219 , HOH B:368 , HOH B:369BINDING SITE FOR RESIDUE MG B 167
08AC8SOFTWAREGLU C:123 , HOH C:288BINDING SITE FOR RESIDUE MG C 170
09AC9SOFTWAREGLU A:129 , GLU D:123BINDING SITE FOR RESIDUE MG D 167
10BC1SOFTWAREASP D:71 , HOH D:170BINDING SITE FOR RESIDUE MG D 168

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OX6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OX6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OX6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OX6)

(-) Exons   (0, 0)

(no "Exon" information available for 2OX6)

(-) 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:162
 aligned with Q8EAP9_SHEON | Q8EAP9 from UniProtKB/TrEMBL  Length:166

    Alignment length:162
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
         Q8EAP9_SHEON     5 IGLNAIEMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPELAQKKLLDIDDIIEMQVLNTTDGIEALFKKEPKRHLAFVVYPTQAIYTQYNPEFLSSLPLTELYNTAAWRIKKECKLVLEVDVSLINLNVEAYKAYREQNGLSESRESRAKWAATQL 166
               SCOP domains d2ox6a1 A:5-166 Hypothetical protein SO3848                                                                                                                        SCOP domains
               CATH domains 2ox6A00 A:5-166 Putative cytoplasmic protein                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhh...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ox6 A   5 IGLNAIEMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPELAQKKLLDIDDIIEMQVLNTTDGIEALFKKEPKRHLAFVVYPTQAIYTQYNPEFLSSLPLTELYNTAAWRIKKECKLVLEVDVSLINLNVEAYKAYREQNGLSESRESRAKWAATQL 166
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  


Chain B from PDB  Type:PROTEIN  Length:162
 aligned with Q8EAP9_SHEON | Q8EAP9 from UniProtKB/TrEMBL  Length:166

    Alignment length:162
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
         Q8EAP9_SHEON     5 IGLNAIEMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPELAQKKLLDIDDIIEMQVLNTTDGIEALFKKEPKRHLAFVVYPTQAIYTQYNPEFLSSLPLTELYNTAAWRIKKECKLVLEVDVSLINLNVEAYKAYREQNGLSESRESRAKWAATQL 166
               SCOP domains d2ox6b_ B: Hypothetical protein SO3848                                                                                                                             SCOP domains
               CATH domains 2ox6B00 B:5-166 Putative cytoplasmic protein                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ox6 B   5 IGLNAIEMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPELAQKKLLDIDDIIEMQVLNTTDGIEALFKKEPKRHLAFVVYPTQAIYTQYNPEFLSSLPLTELYNTAAWRIKKECKLVLEVDVSLINLNVEAYKAYREQNGLSESRESRAKWAATQL 166
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  


Chain C from PDB  Type:PROTEIN  Length:163
 aligned with Q8EAP9_SHEON | Q8EAP9 from UniProtKB/TrEMBL  Length:166

    Alignment length:163
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163   
         Q8EAP9_SHEON     4 NIGLNAIEMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPELAQKKLLDIDDIIEMQVLNTTDGIEALFKKEPKRHLAFVVYPTQAIYTQYNPEFLSSLPLTELYNTAAWRIKKECKLVLEVDVSLINLNVEAYKAYREQNGLSESRESRAKWAATQL 166
               SCOP domains d2ox6c_ C: Hypothetical protein SO3848                                                                                                                              SCOP domains
               CATH domains 2ox6C00 C:4-166 Putative cytoplasmic protein                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhh...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ox6 C   4 NIGLNAIEMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPELAQKKLLDIDDIIEMQVLNTTDGIEALFKKEPKRHLAFVVYPTQAIYTQYNPEFLSSLPLTELYNTAAWRIKKECKLVLEVDVSLINLNVEAYKAYREQNGLSESRESRAKWAATQL 166
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163   


Chain D from PDB  Type:PROTEIN  Length:161
 aligned with Q8EAP9_SHEON | Q8EAP9 from UniProtKB/TrEMBL  Length:166

    Alignment length:161
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 
         Q8EAP9_SHEON     6 GLNAIEMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPELAQKKLLDIDDIIEMQVLNTTDGIEALFKKEPKRHLAFVVYPTQAIYTQYNPEFLSSLPLTELYNTAAWRIKKECKLVLEVDVSLINLNVEAYKAYREQNGLSESRESRAKWAATQL 166
               SCOP domains d2ox6d_ D: Hypothetical protein SO3848                                                                                                                            SCOP domains
               CATH domains 2ox6D00 D:6-166 Putative cytoplasmic protein                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ox6 D   6 GLNAIEMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPELAQKKLLDIDDIIEMQVLNTTDGIEALFKKEPKRHLAFVVYPTQAIYTQYNPEFLSSLPLTELYNTAAWRIKKECKLVLEVDVSLINLNVEAYKAYREQNGLSESRESRAKWAATQL 166
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165
   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 alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OX6)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8EAP9_SHEON | Q8EAP9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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