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(-) Description

Title :  CRYSTAL STRUCTURE OF GH10 ENDO-B-1,4-XYLANASE (XYNB) FROM XANTHOMONAS AXONOPODIS PV CITRI COMPLEXED WITH XYLOSE
 
Authors :  C. R. Santos, V. P. M. Martins, L. M. Zanphorlin, R. Ruller, M. T. Murakam
Date :  22 May 14  (Deposition) - 08 Oct 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Xylanase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. R. Santos, Z. B. Hoffmam, V. P. De Matos Martins, L. M. Zanphorlin, L. H. De Paula Assis, R. V. Honorato, P. S. Lopes De Oliveira, R. Ruller, M. T. Murakami
Molecular Mechanisms Associated With Xylan Degradation By Xanthomonas Plant Pathogens.
J. Biol. Chem. V. 289 32186 2014
PubMed-ID: 25266726  |  Reference-DOI: 10.1074/JBC.M114.605105

(-) Compounds

Molecule 1 - XYLANASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: XYNB, XAC4254
    Organism Scientific: XANTHOMONAS AXONOPODIS PV. CITRI
    Organism Taxid: 190486
    Strain: 306

 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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3XYP2Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3XYP1Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:55 , ASN A:56 , LYS A:59 , GLN A:99 , TRP A:288 , TRP A:295 , GOL A:402 , HOH A:556 , HOH A:561binding site for residue XYP A 401
2AC2SOFTWAREGLU A:138 , TYR A:190 , GLN A:221 , HIS A:223 , GLU A:254 , TRP A:295 , XYP A:401 , HOH A:509 , HOH A:550 , HOH A:556 , HOH A:637binding site for residue GOL A 402
3AC3SOFTWAREGLU A:64 , ASP A:68 , GLU A:115 , GLN A:118 , HOH A:532 , HOH A:538binding site for residue CA A 403
4AC4SOFTWAREGLU B:55 , ASN B:56 , LYS B:59 , GLN B:99 , TRP B:288 , TRP B:295 , GOL B:402 , HOH B:555 , HOH B:567 , HOH B:636binding site for residue XYP B 401
5AC5SOFTWAREGLU B:138 , TYR B:190 , GLN B:221 , HIS B:223 , GLU B:254 , TRP B:295 , XYP B:401 , HOH B:508 , HOH B:555 , HOH B:556binding site for residue GOL B 402
6AC6SOFTWAREGLU B:64 , ASP B:68 , GLU B:115 , GLN B:118 , HOH B:539 , HOH B:540binding site for residue CA B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:92 -Val A:93
2His B:92 -Val B:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PMY)

(-) 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:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeehhhhh.hhhhhh..eee....hhhhhh.......hhhhhhhhhhhhhh....ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee................hhhhhh......hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhh....eeee..hhhhh....hhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhh...eeeeee.......................hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pmy A  23 APLAATASKFLGCAYGAQQAPGFAQYWNKLTPENGGKWGSVEAVRDQMDWSTLDAAYRFAQANQMPFQMHVMVWGNQQPEWIKTLRPAEQRREIEQWFAAVAQRYPDIALLEVVNEPLNDPPSKADTGGGNYLQALGGNGDSGWEWVLQSFRLARRHFPHTKLMINDYSITSSAQATQKYLQIVRLLQRENLVDAIGVQEHAFETTPEVAVSVHRDNLDALAATGLPIYITEFDLDGPTDAQQLADYKRVFPVFWEHPAVHGITLWGFRPGLWRDKEAAYLIRADGTERPALTWLRDYVAAHP 325
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   


Chain B from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeehhhhh.hhhhhh..eee....hhhhhh.......hhhhhhhhhhhhhh....ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee................hhhhhh......hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhh....eeee..hhhhh....hhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhh...eeeeee.......................hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pmy B  23 APLAATASKFLGCAYGAQQAPGFAQYWNKLTPENGGKWGSVEAVRDQMDWSTLDAAYRFAQANQMPFQMHVMVWGNQQPEWIKTLRPAEQRREIEQWFAAVAQRYPDIALLEVVNEPLNDPPSKADTGGGNYLQALGGNGDSGWEWVLQSFRLARRHFPHTKLMINDYSITSSAQATQKYLQIVRLLQRENLVDAIGVQEHAFETTPEVAVSVHRDNLDALAATGLPIYITEFDLDGPTDAQQLADYKRVFPVFWEHPAVHGITLWGFRPGLWRDKEAAYLIRADGTERPALTWLRDYVAAHP 325
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
   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 4PMY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q8PET6_XANAC | Q8PET6: 4pmx 4pmz 4pn2

(-) Related Entries Specified in the PDB File

4pmx THE SAME PROTEIN COMPLEXED WITH XYLOSE.