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- PDB-6dqq: Crystal structure of Haemophilus influenzae OppA complex with end... -

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Basic information

Entry
Database: PDB / ID: 6dqq
TitleCrystal structure of Haemophilus influenzae OppA complex with endogenous peptide
Components
  • ALA-ALA-ALA-ALA
  • Periplasmic oligopeptide-binding protein
KeywordsPEPTIDE BINDING PROTEIN / substrate-binding protein / ABC transporter
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 / 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
ACETATE ION / Periplasmic oligopeptide-binding protein
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 11, 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: ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4567
Polymers59,0872
Non-polymers3695
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-26 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.990, 90.898, 108.778
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: 58784.629 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) / Strain (production host): BL21-DE3 / References: UniProt: Q4QLH0
#2: Protein/peptide ALA-ALA-ALA-ALA


Mass: 302.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.09 Å3/Da / Density % sol: 41.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate pH 4.6 and 2.4M 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: Jun 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 1.85→46.67 Å / Num. obs: 42868 / % possible obs: 99.4 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.022 / Rrim(I) all: 0.082 / Net I/σ(I): 18.6 / Num. measured all: 572217 / Scaling rejects: 13
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.556 / Num. unique obs: 2595 / CC1/2: 0.972 / Rpim(I) all: 0.154 / Rrim(I) all: 0.577 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSJun 1, 2017data reduction
Aimless0.7.1data scaling
BALBES1.0.0phasing
ARP/wARP8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→46.67 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.277 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.128
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 2168 5.1 %RANDOM
Rwork0.1529 ---
obs0.1553 40635 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.13 Å2 / Biso mean: 32.37 Å2 / Biso min: 19 Å2
Baniso -1Baniso -2Baniso -3
1-5.04 Å20 Å20 Å2
2---1.8 Å2-0 Å2
3----3.24 Å2
Refinement stepCycle: final / Resolution: 1.85→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4177 0 22 374 4573
Biso mean--59.01 39.99 -
Num. residues----525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0144313
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173820
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.6645867
X-RAY DIFFRACTIONr_angle_other_deg0.9541.6428960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2223.965227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38515708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6051517
X-RAY DIFFRACTIONr_chiral_restr0.0710.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02798
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 175 -
Rwork0.221 2940 -
all-3115 -
obs--99.58 %

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