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(-) Description

Title :  CRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM GEMMATA OBSCURIGLOBUS
 
Authors :  S. Romero-Romero, A. Rodriguez-Romero, D. A. Fernandez-Velasco
Date :  17 Feb 15  (Deposition) - 15 Jul 15  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Tim Barrel, Isomerase, Tpi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Romero-Romero, M. Costas, A. Rodriguez-Romero, D. Alejandro Fernandez-Velasco
Reversibility And Two State Behaviour In The Thermal Unfolding Of Oligomeric Tim Barrel Proteins.
Phys Chem Chem Phys V. 17 20699 2015
PubMed-ID: 26206330  |  Reference-DOI: 10.1039/C5CP01599E

(-) Compounds

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28B(+)
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TIM
    Organism Scientific: GEMMATA OBSCURIGLOBUS
    Organism Taxid: 114
    Other Details: EXPRESSION TAG: GSH
    Strain: UQM 2246

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2NA3Ligand/IonSODIUM ION
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:14 , LYS A:16 , HIS A:99 , HOH A:530 , HOH A:637binding site for residue NA A 301
2AC2SOFTWAREALA A:175 , ILE A:176 , GLY A:177 , SER A:217 , GLY A:238 , GLY A:239 , HOH A:402 , HOH A:506 , HOH A:529 , HOH A:530binding site for residue PO4 A 303
3AC3SOFTWAREASP A:204 , LYS A:205binding site for residue CA A 304
4AC4SOFTWAREASN B:14 , LYS B:16 , HIS B:99 , GLU B:171 , HOH B:622binding site for residue NA B 301
5AC5SOFTWAREALA B:175 , ILE B:176 , GLY B:177 , SER B:217 , GLY B:238 , GLY B:239 , HOH B:409 , HOH B:516 , HOH B:518 , HOH B:537 , HOH B:622binding site for residue PO4 B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y96)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Y96)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y96)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y96)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y96)

(-) 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhh....eeee...............hhhhhhhhheeeeee.hhhhhhh...hhhhhhhhhhhhhhhh.eeeeee..hhhhhhh.hhhhhhhhhhhhhhh...hhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee......hhhhhhh.....eeeehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y96 A   6 TRKKFVAGNWKMNTTLAEAKALGAAVAKGVTDDRVTVAVFPPYPWLTAVGEVLKGSPVALGAQDVSSEKKGAFTGEVSPAMLLETGCKYALIGHSERRHIIGESETFINHKVHTALEEGLSVVLCMGETLAERERGLQERVFQRQVYAACAGLTDEQFGRIVIAYEPVWAIGTGKVATPEQAQEAHAFVRSKLRLLYGDKIADSTPIVYGGSVTPDNTVGLMSQPDVDGALVGGASLKADSFLAIVKAAG 255
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255


Chain B from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh.....eeee...............hhhhhhhhheeeeee.hhhhhhh...hhhhhhhhhhhhhhhh.eeeeee..hhhhhhh.hhhhhhhhhhhhhh...hhhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee......hhhhhhh.....eeeehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y96 B   6 TRKKFVAGNWKMNTTLAEAKALGAAVAKGVTDDRVTVAVFPPYPWLTAVGEVLKGSPVALGAQDVSSEKKGAFTGEVSPAMLLETGCKYALIGHSERRHIIGESETFINHKVHTALEEGLSVVLCMGETLAERERGLQERVFQRQVYAACAGLTDEQFGRIVIAYEPVWAIGTGKVATPEQAQEAHAFVRSKLRLLYGDKIADSTPIVYGGSVTPDNTVGLMSQPDVDGALVGGASLKADSFLAIVKAAG 255
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255
   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  (0, 0)

(no "SCOP Domain" information available for 4Y96)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y96)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y96)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4Y96)

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  4y96
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  A0A0M3KL18_9 | A0A0M3KL18
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

4y8f 4y90 4y9a