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(-) Description

Title :  NEUTRON CRYSTALLOGRAPHIC STRUCTURE OF A JONESIA DENITRIFICANS LYTIC POLYSACCHARIDE MONOOXYGENASE
 
Authors :  J. -P. Bacik, C. J. Unkefer, J. C. H. Chen
Date :  10 Apr 17  (Deposition) - 24 May 17  (Release) - 31 May 17  (Revision)
Method :  NEUTRON DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Histidine Brace, Hydrolase, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Bacik, S. Mekasha, Z. Forsberg, A. Y. Kovalevsky, G. Vaaje-Kolstad, V. G. H. Eijsink, J. C. Nix, L. Coates, M. J. Cuneo, C. J. Unkefer, J. C. Chen
Neutron And Atomic Resolution X-Ray Structures Of A Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxyge Binding And Evidence For N-Terminal Deprotonation.
Biochemistry V. 56 2529 2017
PubMed-ID: 28481095  |  Reference-DOI: 10.1021/ACS.BIOCHEM.7B00019

(-) Compounds

Molecule 1 - CHITINASE
    Chains: A, B
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 32-173
    Gene: JDEN_1381
    Organism Scientific: JONESIA DENITRIFICANS (STRAIN ATCC 14870 / DSM 20603 / CIP 55134)
    Organism Taxid: 471856
    Strain: ATCC 14870 / DSM 20603 / CIP 55134

 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  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CU2Ligand/IonCOPPER (II) ION
2PER1Ligand/IonPEROXIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2PER-1Ligand/IonPEROXIDE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2PER1Ligand/IonPEROXIDE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:32 , HIS A:109 , HOH A:419binding site for residue CU A 201
2AC2SOFTWAREASN A:159 , HOH A:313 , HIS B:32 , HIS B:109 , PER B:202binding site for residue CU B 201
3AC3SOFTWAREHIS B:32 , GLU B:65 , HIS B:109 , CU B:201 , HOH B:325binding site for residue PER B 202

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:45 -A:54
2A:73 -A:167
3B:45 -B:54
4B:73 -B:167

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:37 -Pro A:38
2Asp B:37 -Pro B:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5VG1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5VG1)

(-) Exons   (0, 0)

(no "Exon" information available for 5VG1)

(-) 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:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhh......hhhhhhh....eee.........hhhhhhhhh.......eee...eeeeeee.....eeeeeeee..eeeeeee........eeeeee.....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vg1 A  32 HGWVTDPPSRQALCASGETSFDCGQISYEPQSVEAPKGATTCSGGNEAFAILDDNSKPWPTTEIASTVDLTWKLTAPHNTSTWEYFVDGQLHQTFDQKGQQPPTSLTHTLTDLPTGEHTILARWNVSNTNNAFYNCMDVVVS 173
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171  


Chain B from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhh......hhhhhhh....eee.........hhhhhhhhh.......eee...eeeeeee.....eeeeeeee..eeeeeee........eeeeee.....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vg1 B  32 HGWVTDPPSRQALCASGETSFDCGQISYEPQSVEAPKGATTCSGGNEAFAILDDNSKPWPTTEIASTVDLTWKLTAPHNTSTWEYFVDGQLHQTFDQKGQQPPTSLTHTLTDLPTGEHTILARWNVSNTNNAFYNCMDVVVS 173
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171
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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 5VG1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5VG1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5VG1)

(-) 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)

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        C7R4I0_JONDD | C7R4I0: 5vg0
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        C7R4I0_JONDD | C7R4I0: 5aa7

(-) Related Entries Specified in the PDB File

5vg0