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- PDB-6i3g: Crystal structure of a putative peptide binding protein AppA from... -

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Basic information

Entry
Database: PDB / ID: 6i3g
TitleCrystal structure of a putative peptide binding protein AppA from Clostridium difficile
ComponentsABC transporter, substrate-binding protein, family 5
KeywordsPEPTIDE BINDING PROTEIN / ABC Transporter / Solute binding protein / AppA
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHughes, A.M. / Wilkinson, A. / Dodson, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J014443/1 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of the putative peptide-binding protein AppA from Clostridium difficile.
Authors: Hughes, A. / Wilson, S. / Dodson, E.J. / Turkenburg, J.P. / Wilkinson, A.J.
History
DepositionNov 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 transporter, substrate-binding protein, family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4983
Polymers55,2751
Non-polymers2232
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-21 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.525, 106.094, 109.515
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 transporter, substrate-binding protein, family 5 / ABC-type transport system / oligopeptide-family solute-binding protein / Oligopeptide-binding ...ABC-type transport system / oligopeptide-family solute-binding protein / Oligopeptide-binding protein AppA / Peptide ABC transporter substrate-binding protein


Mass: 55274.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: appA, appA_1, BGU81_05565, BN1095_250054, BN1096_520027, BN1097_680156, SAMEA3374989_00890
Production host: Escherichia coli (E. coli) / References: UniProt: A0A069AL86
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium iodide, 0.1 M Bis-Tris propane, 20% PEG 3350, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→54.82 Å / Num. obs: 36759 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 27.22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.102 / Net I/σ(I): 13.1
Reflection shellResolution: 2→2.05 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
Aimlessdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→54.82 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.448 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26455 1823 5 %RANDOM
Rwork0.2053 ---
obs0.20822 34874 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.733 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å2-0 Å2
2---2.16 Å20 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 2→54.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3786 0 6 214 4006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133875
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173516
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.6445239
X-RAY DIFFRACTIONr_angle_other_deg1.2691.5788236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5625480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.04525.699193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67115692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.843157
X-RAY DIFFRACTIONr_chiral_restr0.0650.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024334
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
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_it2.6073.7111917
X-RAY DIFFRACTIONr_mcbond_other2.6073.711916
X-RAY DIFFRACTIONr_mcangle_it3.8465.562395
X-RAY DIFFRACTIONr_mcangle_other3.8455.5622396
X-RAY DIFFRACTIONr_scbond_it2.8023.9511958
X-RAY DIFFRACTIONr_scbond_other2.7993.9151952
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3725.7482837
X-RAY DIFFRACTIONr_long_range_B_refined12.7543.4684468
X-RAY DIFFRACTIONr_long_range_B_other10.20443.2364431
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 136 -
Rwork0.338 2524 -
obs--99.92 %

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