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(-) Description

Title :  THE CRYSTAL STRUCTURE OF YFNB FROM BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
 
Authors :  K. Tan, R. Wu, R. Jedrzejczak, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)
Date :  02 Sep 08  (Deposition) - 16 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym./Biol. Unit :  A
Keywords :  Apc60080, Yfnb, Bacillus Subtilis Subsp. Subtilis Str. 168, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, R. Wu, R. Jedrzejczak, A. Joachimiak
The Crystal Structure Of Yfnb From Bacillus Subtilis Subsp. Subtilis Str. 168
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - YFNB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19B
    Expression System Strain: BL21
    Expression System Vector Type: PLASMID
    Gene: YFNB, BSU07330
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: STR. 168

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric/Biological Unit (2, 16)
No.NameCountTypeFull Name
1FMT10Ligand/IonFORMIC ACID
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:18 , TRP A:53 , ARG A:70 , ARG A:92 , HOH A:262 , HOH A:298BINDING SITE FOR RESIDUE FMT A 236
02AC2SOFTWAREASP A:10 , ASN A:123 , LYS A:155 , HOH A:255BINDING SITE FOR RESIDUE FMT A 237
03AC3SOFTWAREGLY A:59 , GLU A:77 , GLY A:152 , GLN A:154 , HOH A:246 , HOH A:422BINDING SITE FOR RESIDUE FMT A 238
04AC4SOFTWAREGLU A:22 , TYR A:45 , LYS A:46 , ASN A:49 , GLN A:50 , HOH A:355BINDING SITE FOR RESIDUE FMT A 239
05AC5SOFTWAREASP A:64 , GLU A:65 , ASN A:68 , HOH A:329BINDING SITE FOR RESIDUE FMT A 240
06AC6SOFTWARELYS A:131 , ARG A:134 , PRO A:213 , THR A:214 , HOH A:373 , HOH A:413BINDING SITE FOR RESIDUE FMT A 241
07AC7SOFTWAREALA A:23 , LEU A:24 , ARG A:27 , HOH A:297BINDING SITE FOR RESIDUE FMT A 242
08AC8SOFTWARETHR A:38 , ASP A:40BINDING SITE FOR RESIDUE FMT A 243
09AC9SOFTWAREASP A:12 , GLY A:124 , HOH A:426BINDING SITE FOR RESIDUE FMT A 244
10BC1SOFTWAREARG A:167 , HOH A:427BINDING SITE FOR RESIDUE FMT A 245

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ED5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:155 -Pro A:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ED5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ED5)

(-) Exons   (0, 0)

(no "Exon" information available for 3ED5)

(-) Sequences/Alignments

Asymmetric/Biological 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:232
 aligned with YFNB_BACSU | O06480 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:232
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230  
           YFNB_BACSU     1 MKRYRTLLFDVDDTILDFQAAEALALRLLFEDQNIPLTNDMKAQYKTINQGLWRAFEEGKMTRDEVVNTRFSALLKEYGYEADGALLEQKYRRFLEEGHQLIDGAFDLISNLQQQFDLYIVTNGVSHTQYKRLRDSGLFPFFKDIFVSEDTGFQKPMKEYFNYVFERIPQFSAEHTLIIGDSLTADIKGGQLAGLDTCWMNPDMKPNVPEIIPTYEIRKLEELYHILNIENT 232
               SCOP domains d3ed5a_ A: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains -3ed5A01        3ed5A02 A:17-100 Putative phosphatase; domain 2                                     3ed5A01 A:2-16,A:101-232  [code=3.40.50.1000, no name defined]                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeee..hhhhhhhhhhhh.hhhhh.eeee.hhh.....hhhhhhhhhhh....hhh.eeeee.....hhhhhhhh..eeeee..............eee.hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ed5 A   1 mKRYRTLLFDVDDTILDFQAAEALALRLLFEDQNIPLTNDmKAQYKTINQGLWRAFEEGKmTRDEVVNTRFSALLKEYGYEADGALLEQKYRRFLEEGHQLIDGAFDLISNLQQQFDLYIVTNGVSHTQYKRLRDSGLFPFFKDIFVSEDTGFQKPmKEYFNYVFERIPQFSAEHTLIIGDSLTADIKGGQLAGLDTCWmNPDmKPNVPEIIPTYEIRKLEELYHILNIENT 232
                            |       10        20        30        40|       50        60|       70        80        90       100       110       120       130       140       150      |160       170       180       190       200   |   210       220       230  
                            |                                      41-MSE              61-MSE                                                                                         157-MSE                                    200-MSE                            
                            1-MSE                                                                                                                                                                                                    204-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, 1)

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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ED5)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YFNB_BACSU | O06480)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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    Lys A:155 - Pro A:156   [ RasMol ]  
 

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 Related Entries

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UniProtKB/Swiss-Prot
        YFNB_BACSU | O06480: 3i76

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