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(-) Description

Title :  CRYSTAL STRUCTURE OF XYLOSE ISOMERASE DOMAIN PROTEIN FROM PLANCTOMYCES LIMNOPHILUS
 
Authors :  Y. Kim, R. Wu, J. Bearden, A. Joachimiak, Midwest Center For Structu Genomics (Mcsg)
Date :  19 Sep 11  (Deposition) - 05 Oct 11  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Tim Barrel, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, R. Wu, J. Bearden, A. Joachimiak
Crystal Structure Of Xylose Isomerase Domain Protein From Planctomyces Limnophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - XYLOSE ISOMERASE DOMAIN PROTEIN TIM BARREL
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3) MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PLIM_1682
    Organism Scientific: PLANCTOMYCES LIMNOPHILUS
    Organism Taxid: 521674
    Strain: DSM 3776

 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  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:155 , ASP A:181 , HIS A:208 , GLU A:256 , GOL A:293BINDING SITE FOR RESIDUE MG A 291
2AC2SOFTWARETYR A:76 , HIS A:119 , ASN A:184 , LEU A:187 , GLU A:258 , GOL A:293BINDING SITE FOR RESIDUE GOL A 292
3AC3SOFTWAREHIS A:119 , GLU A:155 , HIS A:208 , LYS A:210 , GLU A:256 , MG A:291 , GOL A:292BINDING SITE FOR RESIDUE GOL A 293
4AC4SOFTWAREARG A:198 , HOH A:364 , ARG B:173BINDING SITE FOR RESIDUE CL A 294
5AC5SOFTWAREGLU B:155 , ASP B:181 , HIS B:208 , GLU B:256 , HOH B:347BINDING SITE FOR RESIDUE MG B 291
6AC6SOFTWARELYS B:31 , PRO B:33 , THR B:278 , ARG B:281 , HOH B:386BINDING SITE FOR RESIDUE GOL B 293
7AC7SOFTWARETYR B:76 , ASN B:184 , LEU B:187BINDING SITE FOR RESIDUE GOL B 294

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TVA)

(-) 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:282
 aligned with D5SXE5_PLAL2 | D5SXE5 from UniProtKB/TrEMBL  Length:287

    Alignment length:282
                                    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       265       275       285  
         D5SXE5_PLAL2     6 PYWPIGVFTSVDAGLGVHLEVAQDLKVPTVQVHAPHPHTRTREHAQAFRAKCDAAGIQVTVIFGGFDGESYADIPTTARTVGLVPLETRASRVAEMKEISDFASWVGCPAIGLHIGFVPESSSPDYSELVRVTQDLLTHAANHGQAVHLETGQESADHLLEFIEDVNRPNLGINFDPANMILYGTGNPIEALRKVARYVRSIHCKDALWAPVNERGKSWGQEVALGTGDVGMEAYLTTLWEIGYRGPLTIEREIPHDPVQQKKDLASALELLTGLRKKIANC 287
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.......hhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeeeehhhhhhhh...hhhhhhhhhh..eeeeee.eee..hhhhh.....eee.......hhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tva A   6 PYWPIGVFTSVDAGLGVHLEVAQDLKVPTVQVHAPHPHTRTREHAQAFRAKCDAAGIQVTVIFGGFDGESYADIPTTARTVGLVPLETRASRVAEmKEISDFASWVGCPAIGLHIGFVPESSSPDYSELVRVTQDLLTHAANHGQAVHLETGQESADHLLEFIEDVNRPNLGINFDPANmILYGTGNPIEALRKVARYVRSIHCKDALWAPVNERGKSWGQEVALGTGDVGmEAYLTTLWEIGYRGPLTIEREIPHDPVQQKKDLASALELLTGLRKKIANC 287
                                    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       265       275       285  
                                                                                                                         101-MSE                                                                             185-MSE                                             237-MSE                                              


Chain B from PDB  Type:PROTEIN  Length:276
 aligned with D5SXE5_PLAL2 | D5SXE5 from UniProtKB/TrEMBL  Length:287

    Alignment length:284
                                    13        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    
         D5SXE5_PLAL2     4 HKPYWPIGVFTSVDAGLGVHLEVAQDLKVPTVQVHAPHPHTRTREHAQAFRAKCDAAGIQVTVIFGGFDGESYADIPTTARTVGLVPLETRASRVAEMKEISDFASWVGCPAIGLHIGFVPESSSPDYSELVRVTQDLLTHAANHGQAVHLETGQESADHLLEFIEDVNRPNLGINFDPANMILYGTGNPIEALRKVARYVRSIHCKDALWAPVNERGKSWGQEVALGTGDVGMEAYLTTLWEIGYRGPLTIEREIPHDPVQQKKDLASALELLTGLRKKIANC 287
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee........hhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhh...eeeeehhhhhhhh...hhhhhhhhhh..eeeeee.eee..hhhhh.....eee.......hhhhhhhhhhhhh....eee...--------.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tva B   4 HKPYWPIGVFTSVDAGLGVHLEVAQDLKVPTVQVHAPHPHTRTREHAQAFRAKCDAAGIQVTVIFGGFDGESYADIPTTARTVGLVPLETRASRVAEmKEISDFASWVGCPAIGLHIGFVPESSSPDYSELVRVTQDLLTHAANHGQAVHLETGQESADHLLEFIEDVNRPNLGINFDPANmILYGTGNPIEALRKVARYVRSIHCKDALWAPVNERGKSWGQEVALGTGDVGmEAYLTTLWEIGYRGPLTIERE--------KKDLASALELLTGLRKKIANC 287
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183 |     193       203       213       223       233   |   243       253    |    -   |   273       283    
                                                                                                                           101-MSE                                                                             185-MSE                                             237-MSE              258      267
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  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 3TVA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TVA)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (D5SXE5_PLAL2 | D5SXE5)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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