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(-) Description

Title :  CRYSTAL STRUCTURE OF A PROTEIN FROM THE DUF1801 FAMILY (YDHG, BSU05750) FROM BACILLUS SUBTILIS AT 1.75 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  20 Dec 06  (Deposition) - 16 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Secretion Chaperone-Like Fold, 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 (Np_388456. 1) Fro Bacillus Subtilis At 1. 75 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - YDHG PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YDHG
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 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, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL6Ligand/IonGLYCEROL
3MSE6Mod. Amino AcidSELENOMETHIONINE
4SO43Ligand/IonSULFATE ION
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL
3MSE3Mod. Amino AcidSELENOMETHIONINE
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL
3MSE3Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:0 , LEU A:34 , HIS A:35 , THR A:36 , HOH A:215BINDING SITE FOR RESIDUE SO4 A 124
02AC2SOFTWARETHR A:119 , PHE A:120 , TRP A:121 , HOH A:185 , HOH A:210BINDING SITE FOR RESIDUE SO4 A 125
03AC3SOFTWAREPHE A:15 , HIS A:16 , TRP A:94 , ASN A:95 , HOH A:174 , HOH A:211BINDING SITE FOR RESIDUE ACT A 126
04AC4SOFTWARESER A:58 , LYS A:60 , HIS A:61BINDING SITE FOR RESIDUE ACT A 127
05AC5SOFTWAREGLY B:0 , HIS B:35 , THR B:36BINDING SITE FOR RESIDUE SO4 B 124
06AC6SOFTWARETYR A:7 , GLY A:10 , ILE A:11 , VAL A:57BINDING SITE FOR RESIDUE GOL A 128
07AC7SOFTWARETRP A:40 , HIS B:73BINDING SITE FOR RESIDUE GOL A 129
08AC8SOFTWAREGLU A:22 , TRP A:26 , HOH A:155BINDING SITE FOR RESIDUE GOL A 130
09AC9SOFTWAREPHE B:120 , TRP B:121 , LYS B:123BINDING SITE FOR RESIDUE GOL B 125
10BC1SOFTWARETYR B:7 , GLY B:10 , ILE B:11 , VAL B:57 , HOH B:140BINDING SITE FOR RESIDUE GOL B 126
11BC2SOFTWAREGLU B:22 , TRP B:26 , HOH B:148BINDING SITE FOR RESIDUE GOL B 127

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OC6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OC6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OC6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OC6)

(-) Exons   (0, 0)

(no "Exon" information available for 2OC6)

(-) 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:124
 aligned with FRA_BACSU | Q797E6 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:124
                             1                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119    
            FRA_BACSU     - -MDVFSEYLAGIADPFHRERTEEVLTWIKNKYPNLHTEIKWNQPMFTDHGTFIIGFSVSKKHLAVAPEKVTIAHVEDDIVKAGYDYTEQLIRIPWNGPVDYTLLEKMIEFNILDKADCSTFWRK 123
               SCOP domains -d2oc6a1 A:1-123 Uncharacterized protein YdhG                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...eeeee..eeeeee..eeeeeeee...eeeee.hhhhhhhhhhhhhhhh.ee....eeee.....hhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oc6 A   0 GmDVFSEYLAGIADPFHRERTEEVLTWIKNKYPNLHTEIKWNQPmFTDHGTFIIGFSVSKKHLAVAPEKVTIAHVEDDIVKAGYDYTEQLIRIPWNGPVDYTLLEKmIEFNILDKADCSTFWRK 123
                             |       9        19        29        39    |   49        59        69        79        89        99      |109       119    
                             |                                         44-MSE                                                       106-MSE             
                             1-MSE                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with FRA_BACSU | Q797E6 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:124
                             1                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119    
            FRA_BACSU     - -MDVFSEYLAGIADPFHRERTEEVLTWIKNKYPNLHTEIKWNQPMFTDHGTFIIGFSVSKKHLAVAPEKVTIAHVEDDIVKAGYDYTEQLIRIPWNGPVDYTLLEKMIEFNILDKADCSTFWRK 123
               SCOP domains d2oc6b_ B: Uncharacterized protein YdhG                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...eeeee..eeeeee..eeeeeeee...eeeee.hhhhhhhhhhhhhhhh.ee....eeee.....hhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oc6 B   0 GmDVFSEYLAGIADPFHRERTEEVLTWIKNKYPNLHTEIKWNQPmFTDHGTFIIGFSVSKKHLAVAPEKVTIAHVEDDIVKAGYDYTEQLIRIPWNGPVDYTLLEKmIEFNILDKADCSTFWRK 123
                             |       9        19        29        39    |   49        59        69        79        89        99      |109       119    
                             1-MSE                                     44-MSE                                                       106-MSE
   Legend:   → Mismatch (orange background)
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  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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OC6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OC6)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FRA_BACSU | Q797E6)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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