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(-) Description

Title :  X-RAY STRUCTURE ANALYSIS OF XYLANASE - N44D
 
Authors :  Q. Wan, J. M. Park, D. M. Riccardi, L. B. Hanson, Z. Fisher, J. C. Smith, A. Ostermann, T. Schrader, D. E. Graham, L. Coates, P. Langan, A. Y. Kov
Date :  19 Jan 15  (Deposition) - 23 Sep 15  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Jelly Roll, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Wan, J. M. Parks, B. L. Hanson, S. Z. Fisher, A. Ostermann, T. E. Schrader, D. E. Graham, L. Coates, P. Langan, A. Kovalevsky
Direct Determination Of Protonation States And Visualizatio Of Hydrogen Bonding In A Glycoside Hydrolase With Neutron Crystallography.
Proc. Natl. Acad. Sci. Usa V. 112 12384 2015
PubMed-ID: 26392527  |  Reference-DOI: 10.1073/PNAS.1504986112
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE 2
    Chains: A, B
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJEXPRESS401
    Expression System Strain: BL21-GOLD
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: SUBSTRATE-BINDING GROOVE, JELLY ROLL
    Gene: XYN2
    Mutation: YES
    Organism Scientific: HYPOCREA JECORINA
    Organism Taxid: 51453
    Synonym: XYLANASE 2,1,4-BETA-D-XYLAN XYLANOHYDROLASE 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1IOD5Ligand/IonIODIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:82 , SER A:146binding site for residue IOD A 201
2AC2SOFTWARESER A:65 , SER A:184binding site for residue IOD A 202
3AC3SOFTWAREASN B:82 , SER B:146binding site for residue IOD B 201
4AC4SOFTWAREASN B:67 , SER B:184binding site for residue IOD B 202
5AC5SOFTWAREGLY B:24 , THR B:26 , ASN B:38 , HOH B:514binding site for residue IOD B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XQ4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gln A:52 -Pro A:53
2Asn A:82 -Pro A:83
3Gln B:52 -Pro B:53
4Asn B:82 -Pro B:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XQ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XQ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4XQ4)

(-) 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:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eeeeeee.....eeeee....eeeeee....eeeeeeee.......eeeeeeeeeee..eeeeeeeeee...eeeeeeeee.........eeeeeeee..eeeeeeeeeeeee......eeeeeeeeee......eeeehhhhhhhhhhh.....eeeeeeeeeeee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xq4 A   3 IQPGTGYNNGYFYSYWNDGHGGVTYTNGPGGQFSVNWSNSGDFVGGKGWQPGTKNKVINFSGSYNPNGNSYLSVYGWSRNPLIEYYIVENFGTYNPSTGATKLGEVTSDGSVYDIYRTQRVNQPSIIGTATFYQYWSVRRNHRSSGSVNTANHFNAWAQQGLTLGTMDYQIVAVEGYFSSGSASITVS 190
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182        


Chain B from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eeeeeee.....eeeee....eeeeee....eeeeeeee.......eeeeeeeeeee..eeeeeeeeee...eeeeeeeee.........eeeeeeee..eeeeeeeeeeeee......eeeeeeeeee......eeeehhhhhhhhhhh.....eeeeeeeeeeee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xq4 B   3 IQPGTGYNNGYFYSYWNDGHGGVTYTNGPGGQFSVNWSNSGDFVGGKGWQPGTKNKVINFSGSYNPNGNSYLSVYGWSRNPLIEYYIVENFGTYNPSTGATKLGEVTSDGSVYDIYRTQRVNQPSIIGTATFYQYWSVRRNHRSSGSVNTANHFNAWAQQGLTLGTMDYQIVAVEGYFSSGSASITVS 190
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4XQ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XQ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XQ4)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  4xq4
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  XYN2_HYPJR | P36217
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYN2_HYPJR | P36217: 1enx 1red 1ree 1ref 1xyo 1xyp 2d97 2d98 2dfb 2dfc 3lgr 4hk8 4hk9 4hkl 4hko 4hkw 4s2d 4s2f 4s2g 4s2h 4xpv 4xqd 4xqw 5k7p

(-) Related Entries Specified in the PDB File

4xpv 4xqd 4xqw