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- PDB-2x8m: Crystal Structure of CbpF in complex with ipratropium by soaking -

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Basic information

Entry
Database: PDB / ID: 2x8m
TitleCrystal Structure of CbpF in complex with ipratropium by soaking
ComponentsCHOLINE-BINDING PROTEIN F
KeywordsCHOLINE-BINDING PROTEIN / CHOLINE-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 / IPRATROPIUM / Choline-binding protein F
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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: Martin, N.S. / 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: Data collection / Database references ...Data collection / 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 / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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)38,59417
Polymers36,3231
Non-polymers2,27116
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.335, 115.690, 73.201
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, 419 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-X8M / IPRATROPIUM / (3-ENDO,8-ANTI)-3-{[(2R)-3-HYDROXY-2-PHENYLPROPANOYL]OXY}-8-METHYL-8-(1-METHYLETHYL)-8-AZONIABICYCLO[3.2.1]OCTANE


Mass: 332.457 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H30NO3 / Comment: medication, antagonist*YM
#5: Chemical
ChemComp-CHT / CHOLINE ION


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


Mass: 18.015 Da / Num. of mol.: 403 / 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: 23

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 50.83 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→47.68 Å / Num. obs: 38611 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2 / % possible all: 99.5

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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: 1.85→47.68 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1391748.85 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1936 5 %RANDOM
Rwork0.219 ---
obs0.219 38611 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.4633 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2--0.68 Å20 Å2
3----0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.85→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 155 403 3139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg2.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.66
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
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 328 5.3 %
Rwork0.311 5889 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3IPRANEW.PARAMIPRANEW.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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