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(-) Description

Title :  CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS PNEUMONIAE IN THE PRESENCE OF A PEPTIDOGLYCAN ANALOGUE (TETRASACCHARIDE-PENTAPEPTIDE)
 
Authors :  I. Perez-Dorado, R. Molina, J. A. Hermoso, S. Mobashery
Date :  28 Jul 08  (Deposition) - 03 Feb 09  (Release) - 31 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,C#
Biol. Unit 1:  A  (1x)
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Choline-Binding Protein, Cbpf, Peptidoglycan, Choline-Binding-Protein, Lipid-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Molina, A. Gonzalez, M. Stelter, I. Perez-Dorado, R. Kahn, M. Morales, S. Campuzano, N. E. Campillo, S. Mobashery, J. L. Garcia, P. Garcia, J. A. Hermoso
Crystal Structure Of Cbpf, A Bifunctional Choline- Binding Protein And Autolysis Regulator From Streptococcus Pneumoniae.
Embo Rep. V. 10 246 2009
PubMed-ID: 19165143  |  Reference-DOI: 10.1038/EMBOR.2008.245
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHOLINE BINDING PROTEIN F
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: R6

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC#
Biological Unit 1 (1x): A 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1CHT7Ligand/IonCHOLINE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CHT-1Ligand/IonCHOLINE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:130 , TYR A:182 , SER A:207BINDING SITE FOR RESIDUE CHT C 312
2AC2SOFTWARETRP A:276 , TRP A:283 , TYR A:301 , TRP A:309BINDING SITE FOR RESIDUE CHT C 313
3AC3SOFTWARETRP A:255 , TRP A:262 , ASN A:306BINDING SITE FOR RESIDUE CHT C 314
4AC4SOFTWARETRP A:214 , TRP A:221 , TYR A:243 , MET A:251 , ASN A:269BINDING SITE FOR RESIDUE CHT C 315
5AC5SOFTWARETRP A:163 , TRP A:181 , TYR A:202 , ASN A:228BINDING SITE FOR RESIDUE CHT C 316
6AC6SOFTWARETRP A:235 , TRP A:242 , MET A:272 , SER A:289 , HOH C:2002BINDING SITE FOR RESIDUE CHT C 317
7AC7SOFTWARETRP A:194 , TRP A:201 , MET A:231 , SER A:248BINDING SITE FOR RESIDUE CHT C 318

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VYU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VYU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VYU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VYU)

(-) Exons   (0, 0)

(no "Exon" information available for 2VYU)

(-) 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:300
 aligned with Q8DR52_STRR6 | Q8DR52 from UniProtKB/TrEMBL  Length:338

    Alignment length:311
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337 
         Q8DR52_STRR6    28 NTTGGRFVDKDNRKYYVKDDHKAIYWHKIDGKTYYFGDIGEMVVGWQYLEIPGTGYRDNLFDNQPVNEIGLQEKWYYFGQDGALLEQTDKQVLEAKTSENTGKVYGEQYPLSAEKRTYYFDNNYAVKTGWIYEDGNWYYLNKLGNFGDDSYNPLPIGEVAKGWTQDFHVTIDIDRSKPAPWYYLDASGKMLTDWQKVNGKWYYFGSSGSMATGWKYVRGKWYYLDNKNGDMKTGWQYLGNKWYYLRSSGAMVTGWYQDGLTWYYLNAGNGDMKTGWFQVNGKWYYAYSSGALAVNTTVDGYSVNYNGEWVQ 338
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2vyuA0------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2vyuA0------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2vyuA0------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2vyuA0------------------- Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2vyuA0------------------- Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2vyuA0------------------- Pfam domains (6)
           Pfam domains (7) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2vyuA0------------------- Pfam domains (7)
           Pfam domains (8) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2vyuA0------------------- Pfam domains (8)
           Pfam domains (9) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CW_binding_1-2vyuA0------------------- Pfam domains (9)
         Sec.struct. author .....eeeee..eeeeee..eeee.eeee..eeee.........eeeeee.........ee...........eeeeee...........eeeee....................eeeee.........eeeee..eeeee......hhhhh..........eeee..-----------..eeee.........eeee..eeee.........eeeee..eeeee.........eeee....eeee........eeeee..eeeee.........eeeee..eeeee.........eee..eee.....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vyu A   1 NTTGGRFVDKDNRKYYVKDDHKAIYWHKIDGKTYYFGDIGEMVVGWQYLEIPGTGYRDNLFDNQPVNEIGLQEKWYYFGQDGALLEQTDKQVLEAKTSENTGKVYGEQYPLSAEKRTYYFDNNYAVKTGWIYEDGNWYYLNKLGNFGDDSYNPLPIGEVAKGWTQDF-----------APWYYLDASGKMLTDWQKVNGKWYYFGSSGSMATGWKYVRGKWYYLDNKNGDMKTGWQYLGNKWYYLRSSGAMVTGWYQDGLTWYYLNAGNGDMKTGWFQVNGKWYYAYSSGALAVNTTVDGYSVNYNGEWVQ 311
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      |  -       180       190       200       210       220       230       240       250       260       270       280       290       300       310 
                                                                                                                                                                                                167         179
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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 2VYU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VYU)

(-) Pfam Domains  (1, 9)

Asymmetric Unit
(-)
Clan: no clan defined [family: CW_binding_1] (12)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2VYU)

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        Q8DR52_STRR6 | Q8DR52: 2v04 2v05 2x8m 2x8o 2x8p

(-) Related Entries Specified in the PDB File

2v04 CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS PNEUMONIAE
2v05 CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN F FROM STREPTOCOCCUS PNEUMONIAE. CRYSTAL FORM II.