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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE (TM1040_1390) FROM SILICIBACTER SP. TM1040 AT 2.15 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  10 Aug 07  (Deposition) - 21 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Putative Thioesterase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Thioesterase (Yp_613385. 1) From Silicibacter Sp. Tm1040 At 2. 15 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHENYLACETIC ACID DEGRADATION-RELATED PROTEIN
    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
    Gene: YP_613385.1, TM1040_1390
    Organism Scientific: SILICIBACTER SP.
    Organism Taxid: 292414
    Strain: TM1040

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 35)

Asymmetric/Biological Unit (3, 35)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2GOL7Ligand/IonGLYCEROL
3MSE23Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:44 , LEU A:46 , SER A:53 , SER A:56BINDING SITE FOR RESIDUE ACT A 141
02AC2SOFTWAREARG B:90 , LYS B:91 , MSE B:123 , ALA B:125 , HOH B:146BINDING SITE FOR RESIDUE ACT B 141
03AC3SOFTWAREARG B:103 , GLN C:101 , ARG C:103 , ASP C:115BINDING SITE FOR RESIDUE ACT C 141
04AC4SOFTWAREASP C:62 , THR C:81BINDING SITE FOR RESIDUE ACT C 142
05AC5SOFTWAREPHE D:18 , ASP D:62 , TYR D:66BINDING SITE FOR RESIDUE ACT D 141
06AC6SOFTWARELYS D:106 , GLY D:108 , ARG D:109 , THR D:110 , LEU D:111BINDING SITE FOR RESIDUE GOL D 142
07AC7SOFTWARELYS C:106 , GLY C:108 , ARG C:109 , THR C:110 , LEU C:111BINDING SITE FOR RESIDUE GOL C 143
08AC8SOFTWARELYS A:106 , GLY A:108 , ARG A:109 , THR A:110 , LEU A:111BINDING SITE FOR RESIDUE GOL A 142
09AC9SOFTWARELEU A:99 , GLN A:101 , GLY A:122 , MSE A:123 , GLU B:2BINDING SITE FOR RESIDUE GOL A 143
10BC1SOFTWAREHOH A:175 , PHE B:119 , GLU B:121 , GLY B:122 , MSE B:123BINDING SITE FOR RESIDUE GOL B 142
11BC2SOFTWAREARG A:103 , GLN D:101 , ARG D:103 , ASP D:115BINDING SITE FOR RESIDUE GOL D 143
12BC3SOFTWARELYS B:106 , ARG B:109 , THR B:110 , LEU B:111BINDING SITE FOR RESIDUE GOL B 143

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QWZ)

(-) 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:144
 aligned with Q1GGU3_RUEST | Q1GGU3 from UniProtKB/TrEMBL  Length:140

    Alignment length:144
                                  1                                                                                                                                         
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134    
         Q1GGU3_RUEST     - ------MELVFDKDGLSAYLEEVFPQIQGEFSIDALAKGEITMRLNVQERHLRPGGTVSGPSMFALADVSVYALVLAHLGREALAVTTNASLDFMRKPESGRDLLGQARLLKLGRTLAVGDILLFSEGMEAPVARSTMTYSIPP 138
               SCOP domains d2qwza_ A: automated matches                                                                                                                     SCOP domains
               CATH domains -----------2qwzA01 A:6-138  [code=3.10.129.10, no name defined]                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhh..eeeeee...eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.........eeeeeeeeee...eeeeeeeeee.......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qwz A  -5 NLYFQGmELVFDKDGLSAYLEEVFPQIQGEFSIDALAKGEITmRLNVQERHLRPGGTVSGPSmFALADVSVYALVLAHLGREALAVTTNASLDFmRKPESGRDLLGQARLLKLGRTLAVGDILLFSEGmEAPVARSTmTYSIPP 138
                                  |  4        14        24        34  |     44        54  |     64        74        84    |   94       104       114       124       134    
                                  1-MSE                              37-MSE              57-MSE                          89-MSE                           123-MSE  132-MSE  


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with Q1GGU3_RUEST | Q1GGU3 from UniProtKB/TrEMBL  Length:140

    Alignment length:144
                                  1                                                                                                                                         
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134    
         Q1GGU3_RUEST     - ------MELVFDKDGLSAYLEEVFPQIQGEFSIDALAKGEITMRLNVQERHLRPGGTVSGPSMFALADVSVYALVLAHLGREALAVTTNASLDFMRKPESGRDLLGQARLLKLGRTLAVGDILLFSEGMEAPVARSTMTYSIPP 138
               SCOP domains d2qwzb_ B: automated matches                                                                                                                     SCOP domains
               CATH domains -----------2qwzB01 B:6-138  [code=3.10.129.10, no name defined]                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhh..eeeeee...eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.........eeeeeeeeee...eeeeeeeeee.......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qwz B  -5 NLYFQGmELVFDKDGLSAYLEEVFPQIQGEFSIDALAKGEITmRLNVQERHLRPGGTVSGPSmFALADVSVYALVLAHLGREALAVTTNASLDFmRKPESGRDLLGQARLLKLGRTLAVGDILLFSEGmEAPVARSTmTYSIPP 138
                                  |  4        14        24        34  |     44        54  |     64        74        84    |   94       104       114       124       134    
                                  1-MSE                              37-MSE              57-MSE                          89-MSE                           123-MSE  132-MSE  


Chain C from PDB  Type:PROTEIN  Length:138
 aligned with Q1GGU3_RUEST | Q1GGU3 from UniProtKB/TrEMBL  Length:140

    Alignment length:138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        
         Q1GGU3_RUEST     1 MELVFDKDGLSAYLEEVFPQIQGEFSIDALAKGEITMRLNVQERHLRPGGTVSGPSMFALADVSVYALVLAHLGREALAVTTNASLDFMRKPESGRDLLGQARLLKLGRTLAVGDILLFSEGMEAPVARSTMTYSIPP 138
               SCOP domains d2qwzc_ C: automated matches                                                                                                               SCOP domains
               CATH domains -----2qwzC01 C:6-138  [code=3.10.129.10, no name defined]                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh..eeeeeee..eeeeeehhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.........eeeeeeeeee...eeeeeeeeee.......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qwz C   1 mELVFDKDGLSAYLEEVFPQIQGEFSIDALAKGEITmRLNVQERHLRPGGTVSGPSmFALADVSVYALVLAHLGREALAVTTNASLDFmRKPESGRDLLGQARLLKLGRTLAVGDILLFSEGmEAPVARSTmTYSIPP 138
                            |       10        20        30      | 40        50      | 60        70        80        90       100       110       120  |    130 |      
                            1-MSE                              37-MSE              57-MSE                          89-MSE                           123-MSE  132-MSE  


Chain D from PDB  Type:PROTEIN  Length:137
 aligned with Q1GGU3_RUEST | Q1GGU3 from UniProtKB/TrEMBL  Length:140

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
         Q1GGU3_RUEST     2 ELVFDKDGLSAYLEEVFPQIQGEFSIDALAKGEITMRLNVQERHLRPGGTVSGPSMFALADVSVYALVLAHLGREALAVTTNASLDFMRKPESGRDLLGQARLLKLGRTLAVGDILLFSEGMEAPVARSTMTYSIPP 138
               SCOP domains d2qwzd_ D: automated matches                                                                                                              SCOP domains
               CATH domains ----2qwzD01 D:6-138  [code=3.10.129.10, no name defined]                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh......eeeeeee..eeeeee.............hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.........eeeeeeeeee...eeeeeeeeee.......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qwz D   2 ELVFDKDGLSAYLEEVFPQIQGEFSIDALAKGEITmRLNVQERHLRPGGTVSGPSmFALADVSVYALVLAHLGREALAVTTNASLDFmRKPESGRDLLGQARLLKLGRTLAVGDILLFSEGmEAPVARSTmTYSIPP 138
                                    11        21        31     |  41        51     |  61        71        81       |91       101       111       121 |     131|      
                                                              37-MSE              57-MSE                          89-MSE                           123-MSE  132-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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2QWZ)

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