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(-) Description

Title :  STRUCTURE OF RAGB, A MAJOR IMMUNODOMINANT VIRULENCE FACTOR OF PORPHYROMONAS GINGIVALIS.
 
Authors :  T. Goulas, I. Garcia-Ferrer, J. A. Hutcherson, B. A. Potempa, J. Potemp D. A. Scott, F. X. Gomis-Ruth
Date :  28 Jul 15  (Deposition) - 21 Oct 15  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Major Immunodominant Virulence Factor, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Goulas, I. Garcia-Ferrer, J. A. Hutcherson, B. A. Potempa, J. Potempa, D. A. Scott, F. Xavier Gomis-Ruth
Structure Of Ragb, A Major Immunodominant Outer-Membrane Surface Receptor Antigen Of Porphyromonas Gingivalis.
Mol Oral Microbiol V. 31 472 2016
PubMed-ID: 26441291  |  Reference-DOI: 10.1111/OMI.12140

(-) Compounds

Molecule 1 - LIPOPROTEIN RAGB
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 21-501
    Gene: RAGB, PG_0186
    Organism Scientific: PORPHYROMONAS GINGIVALIS (STRAIN ATCC BAA-308 / W83)
    Organism Taxid: 242619
    Strain: ATCC BAA-308 / W83

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 20)

Asymmetric/Biological Unit (6, 20)
No.NameCountTypeFull Name
13DO1Ligand/Ion3-DEOXY-BETA-D-RIBO-HEXOPYRANOSE
2ACT2Ligand/IonACETATE ION
3GOL3Ligand/IonGLYCEROL
4MSE12Mod. Amino AcidSELENOMETHIONINE
5RP31Ligand/Ion3'-DEOXY-D-RIBOFURANOSE-5'-PHOSPHATE
6TG61Ligand/Ion6-O-PHOSPHONO-D-TAGATOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:329 , LEU A:330 , TYR A:331 , GLU A:332 , GLU B:128 , GLU B:215binding site for residue 3DO A 601
2AC2SOFTWAREASP A:46 , TYR A:49 , ALA A:50 , ARG A:53 , LEU A:228 , TYR A:229 , ARG A:290 , GLY A:291 , PHE A:292 , LEU A:297 , HOH A:724 , HOH A:755 , HOH A:797binding site for residue TG6 A 602
3AC3SOFTWAREALA A:98 , ASP A:99 , GLU A:100 , PHE A:111binding site for residue GOL A 603
4AC4SOFTWAREALA A:268 , PHE A:336 , LYS A:410 , ACT A:605 , HOH A:835binding site for residue GOL A 604
5AC5SOFTWAREGLY A:267 , ALA A:269 , GLU A:273 , GOL A:604binding site for residue ACT A 605
6AC6SOFTWARETHR A:296binding site for residue ACT A 606
7AC7SOFTWAREASP A:69 , TRP A:326 , ARG A:438 , ILE A:447 , PHE A:454 , HOH A:892 , ASP B:207 , TYR B:208 , SER B:211 , HOH B:716 , HOH B:717 , HOH B:719 , HOH B:733binding site for residue RP3 B 601
8AC8SOFTWARESER A:139 , ALA A:143 , ASN B:223 , ARG B:224 , ASP B:233 , LYS B:262 , HOH B:767binding site for residue GOL B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CX8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CX8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CX8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CX8)

(-) Exons   (0, 0)

(no "Exon" information available for 5CX8)

(-) 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:472
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eee.......hhhhhh.hhhhhh...ee....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................................hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh.......eeee.........ee......eeee..eeee...eeehhhhhhh....hhhhhh.eeeee....eeee.....hhhhh........ee..eeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhhhh....hhhhh..hhhhh...............hhhhh...hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cx8 A  30 DFQQPYTSFVQTKQNRDGLYALLRNTENPRmHFYQELQSDmYCTTITDGNSLAPFVNWDLGILNDHGRADEDEVSGIAGYYFVYNRLNQQANAFVNNTEAALQNQVYKNSTEIANAKSFLAEGKVLQALAIWRLmDRFSFHESVTEVNSGAKDLGVILLKEYNPGYIGPRATKAQCYDYILSRLSEAIEVLPENRESVLYVSRDYAYALRARIYLALGEYGKAAADAKmVVDKYPLIGAADASEFENIYRSDANNPEIIFRGFASATLGSFTATTLNGAAPAGKDIKYNPSAVPFQWVVDLYENEDFRKSVYIAKVVKKDKGYLVNKFLEDKAYRDVQDKPNLKVGARYFSVAEVYLILVESALQTGDTPTAEKYLKALSKARGAEVSVVNmEALQAERTRELIGEGSRLRDmVRWSIPNNHDAFETQPGLEGFANTTPLKAQAPVGFYAYTWEFPQRDRQTNPQLIKNWPI 501
                                    39        49        59|       69|       79        89        99       109       119       129       139       149       159    |  169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419 |     429       439  |    449       459       469       479       489       499  
                                                         60-MSE    70-MSE                                                                                       164-MSE                                                                                       258-MSE                                                                                                                                                            421-MSE              442-MSE                                                       


Chain B from PDB  Type:PROTEIN  Length:472
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eee.......hhhhhh.hhhhhh...ee....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................................hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh.......eeee.........ee......eeee..eeee...eeehhhhhh.....hhhhh..eeeee....eeee.....hhhhh........ee..eeeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhhhh....hhhhh..hhhhh...............hhhhh...hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cx8 B  30 DFQQPYTSFVQTKQNRDGLYALLRNTENPRmHFYQELQSDmYCTTITDGNSLAPFVNWDLGILNDHGRADEDEVSGIAGYYFVYNRLNQQANAFVNNTEAALQNQVYKNSTEIANAKSFLAEGKVLQALAIWRLmDRFSFHESVTEVNSGAKDLGVILLKEYNPGYIGPRATKAQCYDYILSRLSEAIEVLPENRESVLYVSRDYAYALRARIYLALGEYGKAAADAKmVVDKYPLIGAADASEFENIYRSDANNPEIIFRGFASATLGSFTATTLNGAAPAGKDIKYNPSAVPFQWVVDLYENEDFRKSVYIAKVVKKDKGYLVNKFLEDKAYRDVQDKPNLKVGARYFSVAEVYLILVESALQTGDTPTAEKYLKALSKARGAEVSVVNmEALQAERTRELIGEGSRLRDmVRWSIPNNHDAFETQPGLEGFANTTPLKAQAPVGFYAYTWEFPQRDRQTNPQLIKNWPI 501
                                    39        49        59|       69|       79        89        99       109       119       129       139       149       159    |  169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419 |     429       439  |    449       459       469       479       489       499  
                                                         60-MSE    70-MSE                                                                                       164-MSE                                                                                       258-MSE                                                                                                                                                            421-MSE              442-MSE
   Legend:   → Mismatch (orange background)
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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 5CX8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CX8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CX8)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5CX8)

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