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- PDB-1w9r: Solution Structure of Choline Binding Protein A, Domain R2, the M... -

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Basic information

Entry
Database: PDB / ID: 1w9r
TitleSolution Structure of Choline Binding Protein A, Domain R2, the Major Adhesin of Streptococcus pneumoniae
ComponentsCHOLINE BINDING PROTEIN A
KeywordsRECEPTOR / CBPA / POLYMERIC IMMUNOGLOBULIN RECEPTOR / PIGR / ADHESION / INVASION / PATHOGENESIS
Function / homology
Function and homology information


extracellular region
Similarity search - Function
choline binding protein A / RICH domain / RICH domain superfamily / RICH domain / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / YSIRK type signal peptide / YSIRK Gram-positive signal peptide ...choline binding protein A / RICH domain / RICH domain superfamily / RICH domain / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Choline binding protein A / Choline binding protein A
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodSOLUTION NMR / TAD
AuthorsLuo, R. / Mann, B. / Lewis, W.S. / Rowe, A. / Heath, R. / Stewart, M.L. / Hamburger, A.E. / Bjorkman, P.J. / Sivakolundu, S. / Lacy, E.R. ...Luo, R. / Mann, B. / Lewis, W.S. / Rowe, A. / Heath, R. / Stewart, M.L. / Hamburger, A.E. / Bjorkman, P.J. / Sivakolundu, S. / Lacy, E.R. / Tuomanen, E. / Kriwacki, R.W.
CitationJournal: Embo J. / Year: 2005
Title: Solution Structure of Choline Binding Protein A, the Major Adhesin of Streptococcus Pneumoniae
Authors: Luo, R. / Mann, B. / Lewis, W.S. / Rowe, A. / Heath, R. / Stewart, M.L. / Hamburger, A.E. / Sivakolundu, S. / Lacy, E.R. / Bjorkman, P.J. / Tuomanen, E. / Kriwacki, R.W.
History
DepositionOct 15, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHOLINE BINDING PROTEIN A


Theoretical massNumber of molelcules
Total (without water)13,8271
Polymers13,8271
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 200LEAST ENERGY
Representative

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Components

#1: Protein CHOLINE BINDING PROTEIN A / CBPA-R2


Mass: 13826.608 Da / Num. of mol.: 1 / Fragment: ADHESION DOMAIN RESIDUES 329-443
Source method: isolated from a genetically manipulated source
Details: THE FIRST FOUR RESIDUES (N-TER-GSHM) DERIVE FROM THE PET28A EXPRESSION VECTOR. THE FOLLOWING RESIDUES CORRESPOND TO RESIDUES 329-443 OF CBPA FROM THE TIGR4 STRAIN OF S. PNEUMONIAE.
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97N74, UniProt: A0A0H2US50*PLUS
Sequence detailsTHE PRIMARY ACCESSION NUMBER CORRESPONDS TO THE CBPA PROTEIN SEQUENCE. THIS IS DERIVED FROM THE ...THE PRIMARY ACCESSION NUMBER CORRESPONDS TO THE CBPA PROTEIN SEQUENCE. THIS IS DERIVED FROM THE GENOME SEQUENCE DETERMINED BY TIGR. THAT ENTRY HAS ACCESSION NUMBER AE007507.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CT-HNCA
1213D CT-HN(CO)CA
1313D CT-HN(CA)CB
1413D CT- HN(CO)CACB
1514D HN(CO)CA
1614D HN(CA)CO
1713D C(CO)NH-TOCSY
1813D H(CCO)NH-TOCSY
1913D HBHACBCACONH
11013D (H)CCH-COSY
11113D (H)CCH-TOSCY
11213D NOESY- 1H-15N HSQC
11313D NOESY-1H- 13 CHSQC
11414D 1H-15N HSQC- NOESY-1H-15N HSQC
11514D 1H- 15N HSQC-NOESY-1H-13C HSQC
11614D 1H-13C HSQC-NOESY-1H- 13C HSQC.
NMR detailsText: CBPA-R2 STRUCTURES WERE CALCULATED USING NMR DATA COLLECTED AT 25 C. INTERPROTON DISTANCES WERE ESTIMATED FROM THE VOLUMES OF CROSS-PEAKS IN 3D AND 4D NOESY SPECTRA. THE RESTRAINT LOWER BOUNDS ...Text: CBPA-R2 STRUCTURES WERE CALCULATED USING NMR DATA COLLECTED AT 25 C. INTERPROTON DISTANCES WERE ESTIMATED FROM THE VOLUMES OF CROSS-PEAKS IN 3D AND 4D NOESY SPECTRA. THE RESTRAINT LOWER BOUNDS WERE SET TO THE VAN DER WAALS DISTANCE, AND UPPER BOUNDS WERE SET TO 2.5, 3.5, AND 6.0 FOR STRONG, MEDIUM, AND WEAK RESONANCES, RESPECTIVELY. ESTIMATES OF BACKBONE DIHEDRAL ANGLES F AND Y WERE OBTAINED USING THE PROGRAM TALOS AND 1H , 15N, 13C , 13C , AND 13CO CHEMICAL SHIFT VALUES. TALOS-BASED AND RESTRAINTS WERE USED ONLY WHEN A WELL-DEFINED PREDICTION WAS OBTAINED, AND THIS OCCURRED WITHIN THE HELICAL SEGMENTS OF CBPA-R2. IN ADDITION, H-BOND RESTRAINTS WERE USED WITHIN -HELICES IN THE FOLLOWING WAY. TWO DISTANCE RESTRAINTS WERE USED FOR EACH HYDROGEN BOND, ONE BETWEEN THE HYDROGEN AND THE ACCEPTOR ATOM 1.5-2.3 AND ONE BETWEEN THE DONOR HEAVY ATOM AND THE ACCEPTOR ATOM 2.4-3.3. THESE WERE INTRODUCED AFTER THE INITIAL SET OF STRUCTURE CALCULATIONS. AMIDE PROTONS INVOLVED IN H-BONDS WERE IDENTIFIED ON THE BASIS OF SLOW EXCHANGE WITH D2O. A TOTAL OF 2292 NOE INTERPROTON DISTANCE RESTRAINTS, 83 PAIRS OF AND BACKBONE DIHEDRAL ANGLE RESTRAINTS, AND 146 PAIRS OF H-BOND RESTRAINTS WERE USED TO CALCULATE AN ENSEMBLE OF STRUCTURES USING A MODIFIED VERSION OF THE ORIGINAL TORSION ANGLE DYNAMICS PROTOCOL ROUTINE WITHIN CNS. THE TAD PROTOCOL WAS AS FOLLOWS 75 PS HIGH-TEMPERATURE TAD 50 000 K FOLLOWED BY COOLING TO 1000 K OVER THE COURSE OF 75 PS AND RAMPING OF THE VAN DER WAALS SCALING TERM FROM 0.1 TO 1.0. THE MOLECULES WERE FURTHER COOLED TO 300 K OVER THE COURSE OF 20 PS USING CONVENTIONAL CARTESIAN DYNAMICS FOLLOWED FINALLY BY 10000 STEPS OF CONJUGATE GRADIENT ENERGY MINIMIZATION. THE NOE ENERGY TERM WAS 150 FOR THE FIRST THREE STEPS AND 100 FOR THE LAST. THE DIHEDRAL RESTRAINT TERM WAS 100 FOR THE FIRST THREE STEPS AND 300 FOR THE LAST. TWO HUNDRED STRUCTURES WERE CALCULATED, AND THE LOWEST 40 STRUCTURES WERE FURTHER REFINED BY USING THE SANDER MODULE OF AMBER 8.0 MOLECULAR MODELING SUITE.

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Sample preparation

DetailsContents: 10 MM POTASSIUM PHOSPHATE BUFFER, PH 6.5, 50 MM NACL, 0.02 % (W/V) SODIUM AZIDE, AND 95% H2O/5 % 2H2O (V/V)
Sample conditionsIonic strength: APPROX. 60 MM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS8BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNSstructure solution
RefinementMethod: TAD / Software ordinal: 1
Details: A TOTAL OF 2292 NOE INTERPROTON DISTANCE RESTRAINTS, 83 PAIRS OF PSI AND PHI AND BACKBONE DIHEDRAL ANGLE RESTRAINTS, AND 146 PAIRS OF H-BOND RESTRAINTS WERE USED TO CALCULATE AN ENSEMBLE OF ...Details: A TOTAL OF 2292 NOE INTERPROTON DISTANCE RESTRAINTS, 83 PAIRS OF PSI AND PHI AND BACKBONE DIHEDRAL ANGLE RESTRAINTS, AND 146 PAIRS OF H-BOND RESTRAINTS WERE USED TO CALCULATE AN ENSEMBLE OF STRUCTURES USING A MODIFIED VERSION OF THE ORIGINAL TORSION ANGLE DYNAMICS PROTOCOL ROUTINE WITHIN CNS. THE TAD PROTOCOL WAS AS FOLLOWS. 75 PS HIGH-TEMPERATURE TAD 50000 K FOLLOWED BY COOLING TO 1000 K OVER THE COURSE OF 75 PS AND RAMPING OF THE VAN DER WAALS SCALING TERM FROM 0.1 TO 1.0. THE MOLECULES WERE FURTHER COOLED TO 300 K OVER THE COURSE OF 20 PS USING CONVENTIONAL CARTESIAN DYNAMICS FOLLOWED FINALLY BY 10000 STEPS OF CONJUGATE GRADIENT ENERGY MINIMIZATION. THE NOE ENERGY TERM WAS 150 KCAL PER MOL FOR THE FIRST THREE STEPS AND 100 KCAL PER MOL FOR THE LAST. THE DIHEDRAL RESTRAINT TERM WAS 100 KCAL PER MOL FOR THE FIRST THREE STEPS AND 300 KCAL PER MOL FOR THE LAST. TWO HUNDRED STRUCTURES WERE CALCULATED, AND THE LOWEST 40 STRUCTURES WERE FURTHER REFINED BY USING THE SANDER MODULE OF AMBER 8.0 MOLECULAR MODELING SUITE. THE SOLVENT WAS REPRESENTED BY GENERALIZED-BORN GB SOLVENT MODEL. THE STRUCTURES WERE FIRST ENERGY MINIMIZED FOR1 PS WITHOUT ANY RESTRAINTS FOLLOWED BY 40 PS SIMULATED ANNEALING FROM 400 K TO 0 K WITH ALL THE RESTRAINTS. THE DISTANCE AND ANGLE RESTRAINTS WERE REPRESENTED BY A SQUARE-WELL PENALTY FUNCTION WITH FORCE CONSTANTS OF 20 KCAL PER MOL AND 2 KCAL PER MOL, RESPECTIVELY.
NMR ensembleConformer selection criteria: LEAST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 19

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