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- PDB-6dtf: Crystal structure of Haemophilus influenzae OppA complex with KKK -

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Basic information

Entry
Database: PDB / ID: 6dtf
TitleCrystal structure of Haemophilus influenzae OppA complex with KKK
Components
  • LYS-LYS-LYS
  • Periplasmic oligopeptide-binding protein
KeywordsPEPTIDE BINDING PROTEIN / substrate-binding protein / ABC transporter
Function / homology
Function and homology information


peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / 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 ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Periplasmic oligopeptide-binding protein
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
Haemophilus influenzae 86-028NP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTanaka, K.J. / Pinkett, H.W.
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Oligopeptide-binding protein from nontypeableHaemophilus influenzaehas ligand-specific sites to accommodate peptides and heme in the binding pocket.
Authors: Tanaka, K.J. / Pinkett, H.W.
History
DepositionJun 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 13, 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: Periplasmic oligopeptide-binding protein
B: LYS-LYS-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5854
Polymers60,3932
Non-polymers1922
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-34 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.800, 92.332, 108.362
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Periplasmic oligopeptide-binding protein


Mass: 59987.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain 86-028NP) (bacteria)
Strain: 86-028NP / Gene: oppA, NTHI1292 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4QLH0
#2: Protein/peptide LYS-LYS-LYS


Mass: 405.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus influenzae 86-028NP (bacteria)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 1.98 Å3/Da / Density % sol: 37.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate pH 4.6, 2.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 1.75→46.73 Å / Num. obs: 48105 / % possible obs: 97.9 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.5
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.7 / % possible all: 93.8

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
XDSJan 26, 2018data reduction
BALBES1.0.0phasing
ARP/wARP8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.73 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.236 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.123
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 2341 4.9 %RANDOM
Rwork0.1753 ---
obs0.1776 45707 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.84 Å2 / Biso mean: 40.6 Å2 / Biso min: 25.39 Å2
Baniso -1Baniso -2Baniso -3
1-6.71 Å20 Å20 Å2
2---2.02 Å20 Å2
3----4.69 Å2
Refinement stepCycle: final / Resolution: 1.75→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4133 0 10 249 4392
Biso mean--68.02 45.87 -
Num. residues----517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0144244
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173769
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.6645768
X-RAY DIFFRACTIONr_angle_other_deg0.9331.6418844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5045515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.423.901223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23315709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5591517
X-RAY DIFFRACTIONr_chiral_restr0.0650.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02787
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 172 -
Rwork0.311 3214 -
all-3386 -
obs--94.13 %

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