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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF PROTEIN YXIM_BACSU FROM BACILLUS SUBTILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR595
 
Authors :  A. P. Kuzin, Y. Chen, J. Seetharaman, C. X. Chen, Y. Fang, K. Cunningham, L. -C. Ma, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  28 Nov 06  (Deposition) - 12 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Nesg, X-Ray, Sr595, Yxim, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Kuzin, Y. Chen, J. Seetharaman, C. Chen, Y. Fang, K. Cunningham, L. -C. Ma, R. Xiao, J. Liu, M. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong
X-Ray Structure Of The Hypothetical Protein Yxim_bacsu From Bacillus Subtilis.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YXIM
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: BL21(DE3)+MAGIC

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1MN1Ligand/IonMANGANESE (II) ION
2MSE9Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:19 , SER A:24 , ASP A:65 , HOH A:406 , HOH A:417BINDING SITE FOR RESIDUE MN A 376
2AC2SOFTWAREARG A:100 , LYS A:140BINDING SITE FOR RESIDUE SO4 A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O14)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:177 -Pro A:178

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O14)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O14)

(-) Exons   (0, 0)

(no "Exon" information available for 2O14)

(-) 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:354
 aligned with YXIM_BACSU | P42304 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:354
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378    
           YXIM_BACSU    29 KVYQFDFGSGSMEPGYIGVRASDRYDRSKGYGFQTPENMRDVAASGAGVKSDAVQFLAYGTKSNNTFNVDLPNGLYEVKVTLGNTARASVAAEGVFQVINMTGDGAEDTFQIPVTDGQLNLLVTEGKAGTAFTLSALKIKKLSDQPVTNRTIYVGGDSTVCNYYPLNSSKQAGWGQMLPHYIDKHTFQVRNMASGGQIARGFRNDGQLEAILKYIKPGDYFMLQLGINDTNPKHKESEAEFKEVMRDMIRQVKAKGADVILSTPQGRATDFTSEGIHSSVNRWYRASILALAEEEKTYLIDLNVLSSAYFTSIGPERTLGLYMDGDTLHPNRAGADALARLAVQELKRQGIAGF 382
               SCOP domains d2o14a1 A:14-159 Hypothetical protein YxiM                                                                                                        d2o14a2 A:160-367 Hypothetical protein YxiM                                                                                                                                                                      SCOP domains
               CATH domains 2o14A01 A:14-161  [code=2.60.120.360, no name defined]                                                                                              2o14A02 A:162-367  [code=3.40.50.1110, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------Lipase_GDSL_2-2o14A01 A:167-351                                                                                                                                                          ---------------- Pfam domains
         Sec.struct. author .eeeeee.........eee...........eee.hhh.eeeee...hhhh.eeeee..........eeee...eeeeeeeee....eeeeee..eeeeeeee....eeeeeeee...eeeeeeee.......eeeeeeeeeee.......eeeeee................hhhhhhhhh......eeee......hhhhhhhhhhhhhhhh......eeeee..hhhhhhhhh.hhhhhhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o14 A  14 KVYQFDFGSGSmEPGYIGVRASDRYDRSKGYGFQTPENmRDVAASGAGVKSDAVEFLAYGTKSNNTFNVDLPNGLYEVKVTLGNTARASVAAEGVFQVINmTGDGAEDTFQIPVTDGQLNLLVTEGKAGTAFTLSALKIKKLSDQPVTNRTIYVGGDSTVCNYYPLNSSKQAGWGQmLPHYIDKHTFQVRNmASGGQIARGFRNDGQLEAILKYIKPGDYFmLQLGINDTNPKHKESEAEFKEVmRDmIRQVKAKGADVILSTPQGRATDFTSEGIHSSVNRWYRASILALAEEEKTYLIDLNVLSSAYFTSIGPERTLGLYmDGDTLHPNRAGADALARLAVQELKRQGIAGF 367
                                    23 |      33        43        53        63        73        83        93       103       113|      123       133       143       153       163       173       183      |193       203 |     213       223       233 |     243       253    |  263       273       283       293       303       313       323       333  |    343       353       363    
                                      25-MSE                     52-MSE                                                       114-MSE                                                                     190-MSE        205-MSE                       235-MSE                258-MSE                                                                       336-MSE                           
                                                                                                                                                                                                                                                                                 261-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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: SGNH_hydrolase (17)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YXIM_BACSU | P42304)
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.

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  2o14
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  YXIM_BACSU | P42304
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 Related Entries

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