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- PDB-6hnk: The ligand-free, open structure of CD0873, a substrate binding pr... -

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Basic information

Entry
Database: PDB / ID: 6hnk
TitleThe ligand-free, open structure of CD0873, a substrate binding protein with adhesive properties from Clostridium difficile.
ComponentsABC-type transport system, sugar-family extracellular solute-binding protein
KeywordsTRANSPORT PROTEIN / Substrate binding protein / adhesin / tyrosine binding protein / lipoprotein
Function / homologyABC transporter, substrate-binding protein / ABC transporter substrate binding protein / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ABC-type transport system, sugar-family extracellular solute-binding protein
Function and homology information
Biological speciesPeptoclostridium difficile 630 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBradshaw, W.J. / Kovacs-Simon, A. / Harmer, N.J. / Michell, S.L. / Acharya, K.R.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Molecular features of lipoprotein CD0873: A potential vaccine against the human pathogenClostridioides difficile.
Authors: Bradshaw, W.J. / Bruxelle, J.F. / Kovacs-Simon, A. / Harmer, N.J. / Janoir, C. / Pechine, S. / Acharya, K.R. / Michell, S.L.
History
DepositionSep 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC-type transport system, sugar-family extracellular solute-binding protein


Theoretical massNumber of molelcules
Total (without water)33,9051
Polymers33,9051
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.394, 62.254, 146.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC-type transport system, sugar-family extracellular solute-binding protein


Mass: 33905.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile 630 (bacteria)
Gene: CD630_08730 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q18A65
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium chloride, 7.5% PEG 6000, 7.5% PEG 8,000, 7.5% PEG 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.5→146.1 Å / Num. obs: 12793 / % possible obs: 95.9 % / Redundancy: 8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.079 / Rrim(I) all: 0.177 / Net I/σ(I): 6.2
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1285 / CC1/2: 0.782 / Rpim(I) all: 0.344 / Rrim(I) all: 0.796 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HNI

6hni


Resolution: 2.5→73.05 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / SU B: 20.579 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R: 0.564 / ESU R Free: 0.35 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31012 939 7.4 %RANDOM
Rwork0.25054 ---
obs0.25505 11819 95.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.741 Å2
Baniso -1Baniso -2Baniso -3
1-6.86 Å20 Å20 Å2
2--0.44 Å2-0 Å2
3----7.29 Å2
Refinement stepCycle: 1 / Resolution: 2.5→73.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 0 12 2212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022228
X-RAY DIFFRACTIONr_bond_other_d0.0010.022159
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9833017
X-RAY DIFFRACTIONr_angle_other_deg0.89335056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3545294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.45927.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33215412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.56151
X-RAY DIFFRACTIONr_chiral_restr0.0660.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212445
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02356
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.346.7291179
X-RAY DIFFRACTIONr_mcbond_other3.3396.7281178
X-RAY DIFFRACTIONr_mcangle_it5.41210.0871472
X-RAY DIFFRACTIONr_mcangle_other5.4110.0881473
X-RAY DIFFRACTIONr_scbond_it2.7366.8771049
X-RAY DIFFRACTIONr_scbond_other2.7356.881050
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.72610.2061546
X-RAY DIFFRACTIONr_long_range_B_refined7.5781.0592378
X-RAY DIFFRACTIONr_long_range_B_other7.57281.0782379
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 35 -
Rwork0.403 630 -
obs--67.51 %

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