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(-) Description

Title :  CRYSTAL STRUCTURE OF A GDSL-LIKE LIPASE (BDI_0976) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.93 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  15 Oct 10  (Deposition) - 03 Nov 10  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 6:  A,D  (1x)
Biol. Unit 7:  B,C  (1x)
Keywords :  Serine Hydrolase, Catalytic Triad, Gdsl-Like Lipase, Flavodoxin-Like, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Gdsl-Like Lipase (Bdi_0976) From Parabacteroides Distasonis Atcc 8503 At 1. 93 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GDSL-LIKE LIPASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 25-227
    Gene: BDI_0976
    Organism Scientific: PARABACTEROIDES DISTASONIS
    Organism Taxid: 435591
    Strain: ATCC 8503 / DSM 20701 / NCTC 11152

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 6 (1x): A  D
Biological Unit 7 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 26)

Asymmetric Unit (2, 26)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
2PG42Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 3 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PG4-1Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 4 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PG4-1Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 5 (2, 13)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 6 (2, 13)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 7 (2, 13)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:120 , PHE A:123 , TRP A:169BINDING SITE FOR RESIDUE PG4 A 228
2AC2SOFTWARELYS B:43 , PRO B:45 , SER B:46 , ASN B:47 , ASN B:71 , ARG C:69 , ASN C:70 , ASN C:71BINDING SITE FOR RESIDUE PG4 B 229

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P94)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:44 -Pro A:45
2Val B:44 -Pro B:45
3Val C:44 -Pro C:45
4Val D:44 -Pro D:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P94)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P94)

(-) Exons   (0, 0)

(no "Exon" information available for 3P94)

(-) 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:204
 aligned with A6LAN0_PARD8 | A6LAN0 from UniProtKB/TrEMBL  Length:227

    Alignment length:204
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223    
         A6LAN0_PARD8    24 TEKGDWAQFGRYAEANKTVKVPSNVVFMGNSITDGWWPADSTFFIRNNFVDRGISGQTTSEMLVRFRQDVINLKPKAVVILAGINDIAHNNGVIALENVFGNLVSMAELAKANHIKVIFCSVLPAYDFPWRPGMQPADKVIQLNKWIKEYADKNGLTYVDYHSAMKDERNGLPANLSKDGVHPTLEGYKIMEKIVLEAIHKTVK 227
               SCOP domains d3p94a_ A: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhh.....eeeeeeehhhhhhhhhhh.hhhhhhheeeee....hhhhhhhhhhhhhhhh.eeeeeee.hhhhhh......hhhhhhhhhhhhhhhhhhh..eeeee...............hhhhhhhhhhhhhhhhhhh..eeehhhhhhh.................hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p94 A   0 GEKGDWAQFGRYAEANKTVKVPSNVVFmGNSITDGWWPADSTFFIRNNFVDRGISGQTTSEmLVRFRQDVINLKPKAVVILAGINDIAHNNGVIALENVFGNLVSmAELAKANHIKVIFCSVLPAYDFPWRPGmQPADKVIQLNKWIKEYADKNGLTYVDYHSAmKDERNGLPANLSKDGVHPTLEGYKImEKIVLEAIHKTVK 227
                            ||      33        43       |53        63        73        83 |      93       103       113       123     | 133       143       153   |   163       173       183    |  193       203       213|      223    
                            ||                        51-MSE                            85-MSE                                     129-MSE                     157-MSE                        188-MSE                   214-MSE         
                            0|                                                                                                                                                                                                          
                            25                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:204
 aligned with A6LAN0_PARD8 | A6LAN0 from UniProtKB/TrEMBL  Length:227

    Alignment length:204
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223    
         A6LAN0_PARD8    24 TEKGDWAQFGRYAEANKTVKVPSNVVFMGNSITDGWWPADSTFFIRNNFVDRGISGQTTSEMLVRFRQDVINLKPKAVVILAGINDIAHNNGVIALENVFGNLVSMAELAKANHIKVIFCSVLPAYDFPWRPGMQPADKVIQLNKWIKEYADKNGLTYVDYHSAMKDERNGLPANLSKDGVHPTLEGYKIMEKIVLEAIHKTVK 227
               SCOP domains d3p94b_ B: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhh.....eeeeeeehhhhhhhhhhh.hhhhhhheeeee....hhhhhhhhhhhhhhhh.eeeeeee.hhhhhh......hhhhhhhhhhhhhhhhhhh..eeeee...............hhhhhhhhhhhhhhhhhhh..eeehhhhhhh.................hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p94 B   0 GEKGDWAQFGRYAEANKTVKVPSNVVFmGNSITDGWWPADSTFFIRNNFVDRGISGQTTSEmLVRFRQDVINLKPKAVVILAGINDIAHNNGVIALENVFGNLVSmAELAKANHIKVIFCSVLPAYDFPWRPGmQPADKVIQLNKWIKEYADKNGLTYVDYHSAmKDERNGLPANLSKDGVHPTLEGYKImEKIVLEAIHKTVK 227
                            ||      33        43       |53        63        73        83 |      93       103       113       123     | 133       143       153   |   163       173       183    |  193       203       213|      223    
                            0|                        51-MSE                            85-MSE                                     129-MSE                     157-MSE                        188-MSE                   214-MSE         
                            25                                                                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:200
 aligned with A6LAN0_PARD8 | A6LAN0 from UniProtKB/TrEMBL  Length:227

    Alignment length:200
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226
         A6LAN0_PARD8    27 GDWAQFGRYAEANKTVKVPSNVVFMGNSITDGWWPADSTFFIRNNFVDRGISGQTTSEMLVRFRQDVINLKPKAVVILAGINDIAHNNGVIALENVFGNLVSMAELAKANHIKVIFCSVLPAYDFPWRPGMQPADKVIQLNKWIKEYADKNGLTYVDYHSAMKDERNGLPANLSKDGVHPTLEGYKIMEKIVLEAIHKTV 226
               SCOP domains d3p94c_ C: automated matches                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.....eeeeeeehhhhhhhhhhh.hhhhhhheeeee....hhhhhhhhhhhhhhhh.eeeeeee.hhhhhh......hhhhhhhhhhhhhhhhhhh..eeeee..............hhhhhhhhhhhhhhhhhhhh..eeehhhhhhh.................hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p94 C  27 GDWAQFGRYAEANKTVKVPSNVVFmGNSITDGWWPADSTFFIRNNFVDRGISGQTTSEmLVRFRQDVINLKPKAVVILAGINDIAHNNGVIALENVFGNLVSmAELAKANHIKVIFCSVLPAYDFPWRPGmQPADKVIQLNKWIKEYADKNGLTYVDYHSAmKDERNGLPANLSKDGVHPTLEGYKImEKIVLEAIHKTV 226
                                    36        46    |   56        66        76        86        96       106       116       126  |    136       146       156|      166       176       186 |     196       206       216       226
                                                   51-MSE                            85-MSE                                     129-MSE                     157-MSE                        188-MSE                   214-MSE        


Chain D from PDB  Type:PROTEIN  Length:201
 aligned with A6LAN0_PARD8 | A6LAN0 from UniProtKB/TrEMBL  Length:227

    Alignment length:201
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225 
         A6LAN0_PARD8    26 KGDWAQFGRYAEANKTVKVPSNVVFMGNSITDGWWPADSTFFIRNNFVDRGISGQTTSEMLVRFRQDVINLKPKAVVILAGINDIAHNNGVIALENVFGNLVSMAELAKANHIKVIFCSVLPAYDFPWRPGMQPADKVIQLNKWIKEYADKNGLTYVDYHSAMKDERNGLPANLSKDGVHPTLEGYKIMEKIVLEAIHKTV 226
               SCOP domains d3p94d_ D: automated matches                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------Lipase_GDSL_2-3p94D01 D:49-214                                                                                                                                        ------------ Pfam domains (1)
           Pfam domains (2) -----------------------Lipase_GDSL_2-3p94D02 D:49-214                                                                                                                                        ------------ Pfam domains (2)
           Pfam domains (3) -----------------------Lipase_GDSL_2-3p94D03 D:49-214                                                                                                                                        ------------ Pfam domains (3)
           Pfam domains (4) -----------------------Lipase_GDSL_2-3p94D04 D:49-214                                                                                                                                        ------------ Pfam domains (4)
         Sec.struct. author .........hhhhhh.....eeeeeeehhhhhhhhhhh.hhhhhhheeeee....hhhhhhhhhhhhhhhh.eeeeeee.hhhhhh......hhhhhhhhhhhhhhhhhhh..eeeee...............hhhhhhhhhhhhhhhhhhh..eeehhhhhhh.................hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p94 D  26 KGDWAQFGRYAEANKTVKVPSNVVFmGNSITDGWWPADSTFFIRNNFVDRGISGQTTSEmLVRFRQDVINLKPKAVVILAGINDIAHNNGVIALENVFGNLVSmAELAKANHIKVIFCSVLPAYDFPWRPGmQPADKVIQLNKWIKEYADKNGLTYVDYHSAmKDERNGLPANLSKDGVHPTLEGYKImEKIVLEAIHKTV 226
                                    35        45     |  55        65        75        85        95       105       115       125   |   135       145       155 |     165       175       185  |    195       205       215       225 
                                                    51-MSE                            85-MSE                                     129-MSE                     157-MSE                        188-MSE                   214-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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P94)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: SGNH_hydrolase (17)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3P94)

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