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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CLOSTRIDIUM HISTOLYTICUM COLH COLLAGENASE POLYCYSTIC KIDNEY DISEASE-LIKE DOMAIN 2A IN THE PRESENCE OF CALCIUM AT 1.9 ANGSTROM RESOLUTION
 
Authors :  R. Bauer, K. Janowska, J. Sakon, O. Matsushita, E. Latimer
Date :  31 Jul 14  (Deposition) - 11 Mar 15  (Release) - 10 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  G  (1x)
Biol. Unit 8:  H  (1x)
Keywords :  Calcium-Binding Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Bauer, K. Janowska, K. Taylor, B. Jordan, S. Gann, T. Janowski, E. C. Latimer, O. Matsushita, J. Sakon
Structures Of Three Polycystic Kidney Disease-Like Domains From Clostridium Histolyticum Collagenases Colg And Colh.
Acta Crystallogr. , Sect. D V. 71 565 2015
PubMed-ID: 25760606  |  Reference-DOI: 10.1107/S1399004714027722

(-) Compounds

Molecule 1 - COLH PROTEIN
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(RIL)
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: POLYCYSTIC KIDNEY DISEASE-LIKE DOMAIN (UNP RESIDUES 724- 810)
    Gene: COLH
    Organism Scientific: CLOSTRIDIUM HISTOLYTICUM
    Organism Taxid: 1498
    Synonym: COLLAGENASE

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A       
Biological Unit 2 (1x):  B      
Biological Unit 3 (1x):   C     
Biological Unit 4 (1x):    D    
Biological Unit 5 (1x):     E   
Biological Unit 6 (1x):      F  
Biological Unit 7 (1x):       G 
Biological Unit 8 (1x):        H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 7 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 8 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:685 , SER A:686 , ASP A:713 , ASP A:715 , ASP A:754 , HOH A:927binding site for residue CA A 801
2AC2SOFTWAREASN B:685 , SER B:686 , ASP B:713 , ASP B:715 , ASP B:754 , HOH B:940binding site for residue CA B 801
3AC3SOFTWAREASN C:685 , SER C:686 , ASP C:713 , ASP C:715 , ASP C:754 , HOH C:948binding site for residue CA C 801
4AC4SOFTWAREASN D:685 , SER D:686 , ASP D:713 , ASP D:715 , ASP D:754 , HOH D:929binding site for residue CA D 801
5AC5SOFTWAREASN E:685 , SER E:686 , ASP E:713 , ASP E:715 , ASP E:754 , HOH E:929binding site for residue CA E 801
6AC6SOFTWAREASN F:685 , SER F:686 , ASP F:713 , ASP F:715 , ASP F:754 , HOH F:934binding site for residue CA F 801
7AC7SOFTWAREASN G:685 , SER G:686 , ASP G:713 , ASP G:715 , ASP G:754 , HOH G:954binding site for residue CA G 801
8AC8SOFTWAREASN H:685 , SER H:686 , ASP H:713 , ASP H:715 , ASP H:754 , HOH H:961binding site for residue CA H 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U7K)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:694 -Thr A:695
2Gly B:694 -Thr B:695
3Gly C:694 -Thr C:695
4Gly D:694 -Thr D:695
5Gly E:694 -Thr E:695
6Gly F:694 -Thr F:695
7Gly G:694 -Thr G:695
8Gly H:694 -Thr H:695

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U7K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U7K)

(-) Exons   (0, 0)

(no "Exon" information available for 4U7K)

(-) 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:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee...eee............eeeeeee.....ee.....eee....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4u7k A 685 NSLPYGKINGTYKGTEKEKIKFSSEGSFDPDGKIVSYEWDFGDGNKSNEENPEHSYDKVGTYTVKLKVTDDKGESSVSTTTAEIKD 770
                                   694       704       714       724       734       744       754       764      


Chain B from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee...eee............eeeeeee.....ee.....eee....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4u7k B 685 NSLPYGKINGTYKGTEKEKIKFSSEGSFDPDGKIVSYEWDFGDGNKSNEENPEHSYDKVGTYTVKLKVTDDKGESSVSTTTAEIKD 770
                                   694       704       714       724       734       744       754       764      


Chain C from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee...eee............eeeeeee.....ee.....eee....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4u7k C 685 NSLPYGKINGTYKGTEKEKIKFSSEGSFDPDGKIVSYEWDFGDGNKSNEENPEHSYDKVGTYTVKLKVTDDKGESSVSTTTAEIKD 770
                                   694       704       714       724       734       744       754       764      


Chain D from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee...eee............eeeeeee.....ee.....eee....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4u7k D 685 NSLPYGKINGTYKGTEKEKIKFSSEGSFDPDGKIVSYEWDFGDGNKSNEENPEHSYDKVGTYTVKLKVTDDKGESSVSTTTAEIKD 770
                                   694       704       714       724       734       744       754       764      


Chain E from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee...eee............eeeeeee.....ee.....eee....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4u7k E 685 NSLPYGKINGTYKGTEKEKIKFSSEGSFDPDGKIVSYEWDFGDGNKSNEENPEHSYDKVGTYTVKLKVTDDKGESSVSTTTAEIKD 770
                                   694       704       714       724       734       744       754       764      


Chain F from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee...eee............eeeeeee.....ee.....eee....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4u7k F 685 NSLPYGKINGTYKGTEKEKIKFSSEGSFDPDGKIVSYEWDFGDGNKSNEENPEHSYDKVGTYTVKLKVTDDKGESSVSTTTAEIKD 770
                                   694       704       714       724       734       744       754       764      


Chain G from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee...eee............eeeeeee.....ee.....eee....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4u7k G 685 NSLPYGKINGTYKGTEKEKIKFSSEGSFDPDGKIVSYEWDFGDGNKSNEENPEHSYDKVGTYTVKLKVTDDKGESSVSTTTAEIKD 770
                                   694       704       714       724       734       744       754       764      


Chain H from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee...eee............eeeeeee.....ee.....eee....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4u7k H 685 NSLPYGKINGTYKGTEKEKIKFSSEGSFDPDGKIVSYEWDFGDGNKSNEENPEHSYDKVGTYTVKLKVTDDKGESSVSTTTAEIKD 770
                                   694       704       714       724       734       744       754       764
   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 4U7K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U7K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U7K)

(-) Gene Ontology  (5, 5)

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        Q46085_HATHI | Q46085: 3jqw 3jqx 4ar1 4arf 4jgu 4u6t

(-) Related Entries Specified in the PDB File

4u6t