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- PDB-6ofq: ABC transporter-associated periplasmic binding protein DppA from ... -

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Basic information

Entry
Database: PDB / ID: 6ofq
TitleABC transporter-associated periplasmic binding protein DppA from Helicobacter pylori in complex with peptide STSA
Components
  • Heme-binding protein A / AI-2 binding protein A
  • SER-THR-SER-ALA
KeywordsPeriplasmic peptide binding protein / DppA / type II / periplasmic binding protein
Function / homologyPeptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / ATP-binding cassette (ABC) transporter complex / transmembrane transport / Heme-binding protein A / AI-2 binding protein A
Function and homology information
Biological speciesHelicobacter pylori SS1 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsRahman, M.M. / Machuca, M.A. / Khan, M.F. / Barlow, C.K. / Schittenhelm, R.B. / Roujeinikova, A.
CitationJournal: J.Bacteriol. / Year: 2019
Title: Molecular Basis of Unexpected Specificity of ABC Transporter-Associated Substrate-Binding Protein DppA from Helicobacter pylori.
Authors: Rahman, M.M. / Machuca, M.A. / Khan, M.F. / Barlow, C.K. / Schittenhelm, R.B. / Roujeinikova, A.
History
DepositionMar 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: 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: Heme-binding protein A / AI-2 binding protein A
B: SER-THR-SER-ALA


Theoretical massNumber of molelcules
Total (without water)60,8752
Polymers60,8752
Non-polymers00
Water15,763875
1
A: Heme-binding protein A / AI-2 binding protein A


Theoretical massNumber of molelcules
Total (without water)60,5111
Polymers60,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-2 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.120, 75.770, 128.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAS per the authors the biological assembly is a monomer

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Components

#1: Protein Heme-binding protein A / AI-2 binding protein A


Mass: 60510.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori SS1 (bacteria) / Gene: hbpA, HPYLSS1_00287 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1U9ISL1
#2: Protein/peptide SER-THR-SER-ALA


Mass: 364.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 23% PEG 3350, 0.25 M tri-ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.45→38.92 Å / Num. obs: 95404 / % possible obs: 86.1 % / Redundancy: 2.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.065 / Rrim(I) all: 0.115 / Net I/σ(I): 6.2 / Num. measured all: 239729 / Scaling rejects: 92
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.393 / Num. measured all: 11020 / Num. unique obs: 4613 / CC1/2: 0.751 / Rpim(I) all: 0.297 / Rrim(I) all: 0.497 / Net I/σ(I) obs: 1.9 / % possible all: 84.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F1Q

5f1q


Resolution: 1.45→38.92 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.102 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1751 4656 4.9 %RANDOM
Rwork0.1469 ---
obs0.1483 90711 85.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.37 Å2 / Biso mean: 11.887 Å2 / Biso min: 2.15 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.45→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4146 0 0 875 5021
Biso mean---25.7 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024332
X-RAY DIFFRACTIONr_bond_other_d0.0010.024136
X-RAY DIFFRACTIONr_angle_refined_deg2.1921.965878
X-RAY DIFFRACTIONr_angle_other_deg1.11639557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4175532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52924.316190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46215759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7651516
X-RAY DIFFRACTIONr_chiral_restr0.1380.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214881
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021001
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 349 -
Rwork0.239 6650 -
all-6999 -
obs--85.65 %

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