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- PDB-8are: Crystal structure of the peptide binding protein, OppA, from Baci... -

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Basic information

Entry
Database: PDB / ID: 8are
TitleCrystal structure of the peptide binding protein, OppA, from Bacillus subtilis in complex with a PhrE-derived pentapeptide
Components
  • Oligopeptide-binding protein OppA
  • Phosphatase RapE inhibitor
KeywordsTRANSPORT PROTEIN / Peptide-binding protein Phr peptide Sporulation Bacillus subtilis
Function / homology
Function and homology information


establishment of competence for transformation / peptide transmembrane transporter activity / peptide transport / sporulation resulting in formation of a cellular spore / ATP-binding cassette (ABC) transporter complex / protein transport / outer membrane-bounded periplasmic space / membrane raft / extracellular region / cytoplasm
Similarity search - Function
Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / 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.
Similarity search - Domain/homology
Phosphatase RapE inhibitor / Oligopeptide-binding protein OppA
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHughes, A. / Dodson, E.J. / Wilkinson, A.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Microbiology (Reading, Engl.) / Year: 2022
Title: Peptide transport in Bacillus subtilis - structure and specificity in the extracellular solute binding proteins OppA and DppE.
Authors: Hughes, A.M. / Darby, J.F. / Dodson, E.J. / Wilson, S.J. / Turkenburg, J.P. / Thomas, G.H. / Wilkinson, A.J.
History
DepositionAug 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oligopeptide-binding protein OppA
B: Phosphatase RapE inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9043
Polymers59,8082
Non-polymers961
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-9 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.861, 63.689, 100.060
Angle α, β, γ (deg.)90.000, 114.352, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-919-

HOH

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Components

#1: Protein Oligopeptide-binding protein OppA / Stage 0 sporulation protein KA


Mass: 59231.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Recombinant protein expressed in E. coli. Truncated by 16 residues at N-terminus with vestigial GPA sequence from purification tag.
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: oppA, spo0KA, BSU11430 / Production host: Escherichia coli (E. coli) / References: UniProt: P24141
#2: Protein/peptide Phosphatase RapE inhibitor / Phosphatase regulator E / PhrE


Mass: 576.624 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Recombinant protein expressed in E. coli. Truncated by 16 residues at N-terminus with vestigial GPA sequence from purification tag.
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: phrE, BSU25840 / Production host: Escherichia coli (E. coli) / References: UniProt: O32025
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 41.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Crystals of BsOppA in complex with Ser-Arg-Asn-Val-Thr where grown from the products of an isothermal titration calorimetry experiment. This recovered material was fed into a crystallisation ...Details: Crystals of BsOppA in complex with Ser-Arg-Asn-Val-Thr where grown from the products of an isothermal titration calorimetry experiment. This recovered material was fed into a crystallisation screening experiment in MRC-Wilden 96 well plates. A single crystal of BsOppA-SRNVT was grown from 0.1 M SPG (succinic acid, sodium dihydrogen phosphate, glycine) 25% (w/v) PEG 1500 pH 4.0,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.9→52.263 Å / Num. obs: 37997 / % possible obs: 100 % / Redundancy: 4.1 % / CC1/2: 0.955 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.206 / Rrim(I) all: 0.313 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.11-52.214.30.10615800.9830.090.14
1.9-1.9441.05698540.7580.9331.415

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
REFMAC5.8.0352refinement
ELVESdata processing
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: OppA-SNSS

Resolution: 1.9→52.263 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.841 / WRfactor Rfree: 0.321 / WRfactor Rwork: 0.259 / SU B: 8.531 / SU ML: 0.221 / Average fsc free: 0.8603 / Average fsc work: 0.8809 / Cross valid method: FREE R-VALUE / ESU R: 0.233 / ESU R Free: 0.206
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3084 1811 4.792 %
Rwork0.2518 35978 -
all0.255 --
obs-37789 99.372 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.642 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å2-1.011 Å2
2--1.549 Å2-0 Å2
3----1.499 Å2
Refinement stepCycle: LAST / Resolution: 1.9→52.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4060 0 5 220 4285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124172
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163684
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.6485664
X-RAY DIFFRACTIONr_angle_other_deg0.4781.5658622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0845513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.198510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39410690
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.82110203
X-RAY DIFFRACTIONr_chiral_restr0.0650.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024725
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02799
X-RAY DIFFRACTIONr_nbd_refined0.2180.2844
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.23623
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22050
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22172
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0410.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.27
X-RAY DIFFRACTIONr_nbd_other0.2180.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.26
X-RAY DIFFRACTIONr_mcbond_it1.0561.6472055
X-RAY DIFFRACTIONr_mcbond_other1.0561.6472055
X-RAY DIFFRACTIONr_mcangle_it1.672.4662567
X-RAY DIFFRACTIONr_mcangle_other1.672.4662568
X-RAY DIFFRACTIONr_scbond_it1.3151.7482117
X-RAY DIFFRACTIONr_scbond_other1.3011.7442114
X-RAY DIFFRACTIONr_scangle_it2.0792.5673097
X-RAY DIFFRACTIONr_scangle_other2.0742.5613092
X-RAY DIFFRACTIONr_lrange_it3.17120.5874804
X-RAY DIFFRACTIONr_lrange_other3.09920.4154775
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.9-1.9490.5611520.5626330.5627950.3180.32699.64220.531
1.949-2.0030.3491220.30426050.30627270.9090.921000.304
2.003-2.0610.3431200.2925190.29226440.9160.93499.81090.29
2.061-2.1240.3361300.26724500.2725800.9260.9451000.266
2.124-2.1930.31350.26223770.26425120.9340.9431000.262
2.193-2.270.5861040.55421370.55523950.4530.43793.56990.544
2.27-2.3560.3021170.26521710.26722940.9240.93399.73840.272
2.356-2.4520.2991070.21321680.21722750.9330.9681000.215
2.452-2.560.2711170.20320270.20721460.9540.97199.90680.205
2.56-2.6850.295930.20619690.2120620.950.9721000.213
2.685-2.830.258780.2118740.21219520.950.9711000.217
2.83-3.0010.306810.21518050.2218860.9450.9691000.225
3.001-3.2080.274860.21816410.22117270.9450.971000.231
3.208-3.4630.281760.21715590.2216360.9430.9799.93890.232
3.463-3.7920.369420.26414050.26714900.910.95397.11410.278
3.792-4.2370.192590.17213190.17313810.9810.98299.78280.194
4.237-4.8870.202620.13811440.14112070.9760.9999.91720.16
4.887-5.9730.191530.1579840.15910380.980.98999.90370.182
5.973-8.3920.178520.1427500.1458020.9790.9891000.163
8.392-52.2630.208250.1544410.1574670.9680.98599.78590.177

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