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(-) Description

Title :  CRYSTAL STRUCTURE OF A MUTANT (665I6H) OF THE C-TERMINAL DOMAIN OF RGPB
 
Authors :  I. De Diego, M. Ksiazek, D. Mizgalska, P. Golik, B. Szmigielski, M. Now Z. Nowakowska, B. Potempa, L. Koneru, K. A. Nguyen, J. Enghild, I. B. Th G. Dubin, F. X. Gomis-Ruth, J. Potempa
Date :  29 Jan 15  (Deposition) - 06 Apr 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Type Ix Secretion System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. De Diego, M. Ksiazek, D. Mizgalska, L. Koneru, P. Golik, B. Szmigielski, M. Nowak, Z. Nowakowska, B. Potempa, J. A. Houston, J. J. Enghild, I. B. Thogersen, J. Gao, A. H. Kwan, J. Trewhella, G. Dubin, F. X. Gomis-Ruth, K. Nguyen, J. Potempa
The Outer-Membrane Export Signal Of Porphyromonas Gingivalis Type Ix Secretion System (T9Ss) Is A Conserved C-Terminal Beta-Sandwich Domain.
Sci. Rep. V. 6 23123 2016
PubMed-ID: 27005013  |  Reference-DOI: 10.1038/SREP23123

(-) Compounds

Molecule 1 - GINGIPAIN R2
    Chains: A, B
    EC Number: 3.4.22.37
    Fragment: IGSF AND CTD DOMAINS, RESIDUES 577-736
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 242619
    Other Details: HEXAHISTIDINE INSERTION AFTER SER 664
    Strain: W83
    Synonym: ARG-GINGIPAIN, GINGIPAIN 2, RGP-2, ARG-GINGIPAIN B

 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, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2099 , HOH A:2100 , HOH A:2101 , HOH A:2125 , HOH A:2126 , ASN B:707 , ARG B:708BINDING SITE FOR RESIDUE SO4 A1737
2AC2SOFTWAREASN A:707 , ARG A:708 , HOH A:2102 , PRO B:580 , LYS B:706 , ASN B:707 , HOH B:2061BINDING SITE FOR RESIDUE SO4 A1738
3AC3SOFTWAREGLU A:661 , GLY A:662 , ARG A:721 , THR A:728 , HOH A:2114BINDING SITE FOR RESIDUE SO4 A1739
4AC4SOFTWAREGLU B:661 , GLY B:662 , ARG B:721 , ALA B:723 , THR B:728 , HOH B:2100BINDING SITE FOR RESIDUE SO4 B1737
5AC5SOFTWAREPRO B:588 , ALA B:589 , ASN B:590 , HOH B:2107BINDING SITE FOR RESIDUE SO4 B1738
6AC6SOFTWAREPRO A:588 , ALA A:589 , ASN A:590 , HOH A:2011 , HOH A:2127BINDING SITE FOR RESIDUE GOL A1740
7AC7SOFTWAREASP A:696 , ASN A:698 , ARG A:700 , ASN B:641BINDING SITE FOR RESIDUE GOL A1741

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AG8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5AG8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AG8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AG8)

(-) Exons   (0, 0)

(no "Exon" information available for 5AG8)

(-) 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:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee...eee....eeeeee.....eeeeee..eeeeeee....eeeee.........eeeeeee......eeeeeeee....eeeee..eeeeeeeeeeeeee.....eeeeeeeeeeee...eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ag8 A 579 VPTKMQVTAPANISASAQTFEVACDYNGAIATLSDDGDMVGTAIVKDGKAIIKLNESIADETNLTLTVVGYNKVTVIKDVKVEGKPYTVAVSGKTITVESPAAGLTIFDMNGRRVATAKNRMVFEAQNGVYAVRIATEGKTYTEKVIVK 736
                                   588       598       608       618       628       638       648       658   ||  677       687       697       707       717       727         
                                                                                                             662|                                                                
                                                                                                              672                                                                


Chain B from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee...eee....eeeeee.....eeeeee..eeeeeee....eeeee.........eeeeeee......eeeeeeee....eeeee..eeeeeeeeeeeeee.....eeeeeeeeeeee...eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ag8 B 579 VPTKMQVTAPANISASAQTFEVACDYNGAIATLSDDGDMVGTAIVKDGKAIIKLNESIADETNLTLTVVGYNKVTVIKDVKVEGKPYTVAVSGKTITVESPAAGLTIFDMNGRRVATAKNRMVFEAQNGVYAVRIATEGKTYTEKVIVK 736
                                   588       598       608       618       628       638       648       658   ||  677       687       697       707       717       727         
                                                                                                             662|                                                                
                                                                                                              672
   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 5AG8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AG8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AG8)

(-) Gene Ontology  (7, 7)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CPG2_PORGI | P95493: 1cvr 4ief 5ag9 5hfs

(-) Related Entries Specified in the PDB File

5ag9 CRYSTAL STRUCTURE OF A MUTANT (665SXA) C-TERMINAL DOMAIN OF RGPB
5agb CRYSTAL STRUCTURE OF A MUTATED (666I6H) C-TERMINAL DOMAIN OF RGPB