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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A FAT ACID (STEARIC ACID)-BINDING PROTEIN FROM EUBACTERIUM VENTRIOSUM ATCC 27560.
 
Authors :  R. Zhang, K. Tan, H. Li, L. Keigher, G. Babnigg, A. Joachimiak, Midwest For Structural Genomics (Mcsg)
Date :  15 Jul 10  (Deposition) - 22 Sep 10  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Stearic Acid, Degv Family Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, K. Tan, H. Li, L. Keigher, G. Babnigg, A. Joachimiak
The Crystal Structure Of A Fat Acid (Stearic Acid)-Binding Protein From Eubacterium Ventriosum Atcc 27560.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FAT ACID-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MCSG19
    Expression System Strain: PPK1037
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EUBVEN_01190
    Organism Scientific: EUBACTERIUM VENTRIOSUM
    Organism Taxid: 411463
    Strain: ATCC 27560

 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  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2STE2Ligand/IonSTEARIC ACID
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2STE1Ligand/IonSTEARIC ACID
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2STE1Ligand/IonSTEARIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:27 , THR A:62 , SER A:63 , LEU A:64 , PHE A:93 , SER A:94 , ASN A:124 , THR A:125 , PHE A:163 , ILE A:269 , HIS A:276 , GLY A:283 , HOH A:315 , HOH B:370BINDING SITE FOR RESIDUE STE A 301
2AC2SOFTWARELEU B:27 , THR B:62 , SER B:63 , LEU B:64 , PHE B:93 , SER B:94 , ASN B:124 , THR B:125 , PHE B:163 , ARG B:176 , ILE B:269 , HIS B:276 , GLY B:283 , HOH B:303 , HOH B:336 , HOH B:372BINDING SITE FOR RESIDUE STE B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NYI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NYI)

(-) 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:293
 aligned with A5Z657_9FIRM | A5Z657 from UniProtKB/TrEMBL  Length:293

    Alignment length:293
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290   
         A5Z657_9FIRM     1 MYKIVSDSACDLSKEYLEKHDVTIVPLSVSFDGETYYRDGVDITRDECYQRMVDDPKLFPKTSLPSVESYADVFRSFVEQGFPVVCFTITTLFSGSYNSAINAKSLVLEDYPDANICVIDSKQNTVTQALLIDQFVRMLEDGLSFEQAMSKLDALMASARIFFTVGSLDYLKMGGRIGKVATAATGKLGVKPVIIMKDGDIGLGGIGRNRNKLKNSVLQVAKKYLDENNKDNFIVSVGYGYDKEEGFEFMKEVESTLDVKLDSETNVAIGIVSAVHTGPYPIGLGVIRKYETL 293
               SCOP domains d3nyia_ A: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhh.hhhhhhhhheeee..eee.....eee.....hhhhhhhhhhhh.....eee..hhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhheeeee...hhhhhhh..hhhhh.hhhhh...eeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhh...hhhhhee.hhhhhhhhh...eeeeeee.hhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nyi A   1 mYKIVSDSACDLSKEYLEKHDVTIVPLSVSFDGETYYRDGVDITRDECYQRmVDDPKLFPKTSLPSVESYADVFRSFVEQGFPVVCFTITTLFSGSYNSAINAKSLVLEDYPDANICVIDSKQNTVTQALLIDQFVRmLEDGLSFEQAmSKLDALmASARIFFTVGSLDYLKmGGRIGKVATAATGKLGVKPVIImKDGDIGLGGIGRNRNKLKNSVLQVAKKYLDENNKDNFIVSVGYGYDKEEGFEFmKEVESTLDVKLDSETNVAIGIVSAVHTGPYPIGLGVIRKYETL 293
                            |       10        20        30        40        50 |      60        70        80        90       100       110       120       130       140       150     | 160       170  |    180       190     | 200       210       220       230       240       250       260       270       280       290   
                            |                                                 52-MSE                                                                               138-MSE    149-MSE  |              173-MSE                196-MSE                                               250-MSE                                       
                            1-MSE                                                                                                                                                    156-MSE                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:295
 aligned with A5Z657_9FIRM | A5Z657 from UniProtKB/TrEMBL  Length:293

    Alignment length:295
                              1                                                                                                                                                                                                                                                                                                    
                              |      8        18        28        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     
         A5Z657_9FIRM     - --MYKIVSDSACDLSKEYLEKHDVTIVPLSVSFDGETYYRDGVDITRDECYQRMVDDPKLFPKTSLPSVESYADVFRSFVEQGFPVVCFTITTLFSGSYNSAINAKSLVLEDYPDANICVIDSKQNTVTQALLIDQFVRMLEDGLSFEQAMSKLDALMASARIFFTVGSLDYLKMGGRIGKVATAATGKLGVKPVIIMKDGDIGLGGIGRNRNKLKNSVLQVAKKYLDENNKDNFIVSVGYGYDKEEGFEFMKEVESTLDVKLDSETNVAIGIVSAVHTGPYPIGLGVIRKYETL 293
               SCOP domains d3nyib_ B: automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------DegV-3nyiB01 B:72-289                                                                                                                                                                                                     ---- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------DegV-3nyiB02 B:72-289                                                                                                                                                                                                     ---- Pfam domains (2)
         Sec.struct. author ....eeeee.hhh.hhhhhhhhheeee..eee.....eee.....hhhhhhhhhhhh.....eee..hhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhheeeee...hhhhhhhh.hhhhhhhhhhh...eeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhh...hhhhhee.hhhhhhhhh...eeeeeee.hhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nyi B  -1 NAmYKIVSDSACDLSKEYLEKHDVTIVPLSVSFDGETYYRDGVDITRDECYQRmVDDPKLFPKTSLPSVESYADVFRSFVEQGFPVVCFTITTLFSGSYNSAINAKSLVLEDYPDANICVIDSKQNTVTQALLIDQFVRmLEDGLSFEQAmSKLDALmASARIFFTVGSLDYLKmGGRIGKVATAATGKLGVKPVIImKDGDIGLGGIGRNRNKLKNSVLQVAKKYLDENNKDNFIVSVGYGYDKEEGFEFmKEVESTLDVKLDSETNVAIGIVSAVHTGPYPIGLGVIRKYETL 293
                              |      8        18        28        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     
                              1-MSE                                             52-MSE                                                                               138-MSE    149-MSE  |              173-MSE                196-MSE                                               250-MSE                                       
                                                                                                                                                                                       156-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NYI)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: EDD (22)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A5Z657_9FIRM | A5Z657)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.

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