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- PDB-2x8p: Crystal Structure of CbpF in Complex with Atropine by Co- Crystal... -

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Basic information

Entry
Database: PDB / ID: 2x8p
TitleCrystal Structure of CbpF in Complex with Atropine by Co- Crystallization
ComponentsCHOLINE-BINDING PROTEIN F
KeywordsCHOLINE-BINDING PROTEIN / LIPID-BINDING-PROTEIN
Function / homology
Function and homology information


left handed beta-beta-3-solenoid - #20 / Cholin Binding / left handed beta-beta-3-solenoid / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
CHOLINE ION / Chem-OIN / Choline-binding protein F
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsSilva-Martin, N. / Hermoso, J.A.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Crystal Structures of Cbpf Complexed with Atropine and Ipratropium Reveal Clues for the Design of Novel Antimicrobials Against Streptococcus Pneumoniae.
Authors: Silva-Martin, N. / Retamosa, M.G. / Maestro, B. / Bartual, S.G. / Rodes, M.J. / Garcia, P. / Sanz, J.M. / Hermoso, J.A.
History
DepositionMar 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references / Non-polymer description ...Database references / Non-polymer description / Refinement description / Version format compliance
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _citation_author.name / _database_2.pdbx_DOI ..._citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHOLINE-BINDING PROTEIN F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,70311
Polymers36,3231
Non-polymers1,38010
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.540, 116.077, 73.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CHOLINE-BINDING PROTEIN F


Mass: 36322.938 Da / Num. of mol.: 1 / Fragment: RESIDUES 28-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Plasmid: PIN-III-A3 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8DR52

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Non-polymers , 5 types, 284 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OIN / (1R,5S)-8-METHYL-8-AZABICYCLO[3.2.1]OCT-3-YL (2R)-3-HYDROXY-2-PHENYLPROPANOATE / ATROPINE


Mass: 289.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H14NO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 13

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.12 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: MARRESEARCH / Wavelength: 1.54179
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.27→24.73 Å / Num. obs: 16653 / % possible obs: 79.5 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 2.1
Reflection shellResolution: 2.27→2.43 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 79.5

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V05

2v05


Resolution: 2.27→24.73 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2073491.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1154 6.9 %RANDOM
Rwork0.226 ---
obs0.226 16653 77.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.16 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.73 Å20 Å20 Å2
2--0.8 Å20 Å2
3---2.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.27→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 94 274 2949
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.44
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.27→2.41 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 187 7.1 %
Rwork0.327 2455 -
obs--75.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMAATRO.TOP
X-RAY DIFFRACTION4AATRO.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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