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

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Basic information

Entry
Database: PDB / ID: 8arn
TitleCrystal structure of the peptide binding protein, OppA, from Bacillus subtilis in complex with an endogenous tetrapeptide
Components
  • Endogenous tetrapeptide (SER-ASN-SER-SER)
  • Oligopeptide-binding protein OppA
KeywordsTRANSPORT PROTEIN / Peptide-binding protein / Sporulation Bacillus subtilis
Function / homology
Function and homology information


establishment of competence for transformation / peptide transport / peptide transmembrane transporter activity / sporulation resulting in formation of a cellular spore / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / protein transport / outer membrane-bounded periplasmic space / membrane raft
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
Oligopeptide-binding protein OppA
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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: Oligopeptide-binding protein OppA
C: Endogenous tetrapeptide (SER-ASN-SER-SER)
D: Endogenous tetrapeptide (SER-ASN-SER-SER)


Theoretical massNumber of molelcules
Total (without water)119,2494
Polymers119,2494
Non-polymers00
Water15,925884
1
A: Oligopeptide-binding protein OppA
C: Endogenous tetrapeptide (SER-ASN-SER-SER)


Theoretical massNumber of molelcules
Total (without water)59,6252
Polymers59,6252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oligopeptide-binding protein OppA
D: Endogenous tetrapeptide (SER-ASN-SER-SER)


Theoretical massNumber of molelcules
Total (without water)59,6252
Polymers59,6252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.520, 65.890, 153.290
Angle α, β, γ (deg.)90.000, 100.970, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 59231.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Recombinant protein purified from E. coli with a co-purifying tetrapeptide ligand SNSS
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 Endogenous tetrapeptide (SER-ASN-SER-SER)


Mass: 393.351 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Peptide co-purifying with the recombinant protein and bound in the peptide binding cleft
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 884 / 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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Crystals of OppA were obtained from hanging drops composed of 2 microlitres of reservoir solution consisting of 0.1 M MMT, 22.5% PEG 1500 and 2.5% DMSO pH 8.0 and 2 microlitres protein at 18 ...Details: Crystals of OppA were obtained from hanging drops composed of 2 microlitres of reservoir solution consisting of 0.1 M MMT, 22.5% PEG 1500 and 2.5% DMSO pH 8.0 and 2 microlitres protein at 18 mg.ml-1 with crystal optimisation following a seeding protocol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.82 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82 Å / Relative weight: 1
ReflectionResolution: 1.5→55.025 Å / Num. obs: 158694 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.038 / Rrim(I) all: 0.059 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.22-54.963.70.03710280.9960.0310.049
1.5-1.534.20.72378290.6090.6170.955

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
REFMAC5.8.0352refinement
DIALSdata reduction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RKM

1rkm


Resolution: 1.5→55.025 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.752 / SU ML: 0.063 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2066 7849 4.946 %
Rwork0.1772 150844 -
all0.179 --
obs-158693 99.861 %
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: 22.694 Å2
Baniso -1Baniso -2Baniso -3
1--0.661 Å20 Å2-0.283 Å2
2--1.266 Å20 Å2
3----0.461 Å2
Refinement stepCycle: LAST / Resolution: 1.5→55.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8171 0 0 884 9055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0128375
X-RAY DIFFRACTIONr_bond_other_d0.0050.0167521
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.64911342
X-RAY DIFFRACTIONr_angle_other_deg0.5571.5717641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49451025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.4518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.791101474
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.00210403
X-RAY DIFFRACTIONr_chiral_restr0.0840.21201
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021583
X-RAY DIFFRACTIONr_nbd_refined0.2210.21446
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.26894
X-RAY DIFFRACTIONr_nbtor_refined0.1820.24100
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24287
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2485
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.265
X-RAY DIFFRACTIONr_nbd_other0.1780.2205
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.2230
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0080.21
X-RAY DIFFRACTIONr_mcbond_it1.9752.2914106
X-RAY DIFFRACTIONr_mcbond_other1.9742.2914106
X-RAY DIFFRACTIONr_mcangle_it2.5613.4375129
X-RAY DIFFRACTIONr_mcangle_other2.5613.4375130
X-RAY DIFFRACTIONr_scbond_it3.1512.5664269
X-RAY DIFFRACTIONr_scbond_other3.1512.5664270
X-RAY DIFFRACTIONr_scangle_it4.6663.7046213
X-RAY DIFFRACTIONr_scangle_other4.6663.7046214
X-RAY DIFFRACTIONr_lrange_it17.09360.969681
X-RAY DIFFRACTIONr_lrange_other15.46158.1859438
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
1.5-1.5390.2975740.296111020.296116910.9330.93299.87170.289
1.539-1.5810.3065430.276108030.277113590.9260.94299.88560.264
1.581-1.6270.2935190.254105790.256111020.9390.95399.9640.241
1.627-1.6770.2665430.229102460.231107930.9550.96399.96290.214
1.677-1.7320.2575250.21899230.22104610.9540.96899.87570.202
1.732-1.7930.254980.21295910.214100890.9590.9711000.195
1.793-1.860.2434780.20691820.20896680.9620.97399.91730.189
1.86-1.9360.2354780.19689510.19894310.9640.97599.97880.181
1.936-2.0220.2324920.20385540.20490550.9640.97499.90060.192
2.022-2.120.2184600.18981060.19185760.9710.97899.88340.182
2.12-2.2350.2243510.18478610.18682160.970.97999.95130.181
2.235-2.370.1923820.17273560.17377510.9770.98199.83230.174
2.37-2.5340.1933530.16369880.16573460.9780.98499.93190.169
2.534-2.7360.2093430.17164650.17368140.9720.98299.91190.182
2.736-2.9970.213260.17259230.17462600.9720.98299.82430.188
2.997-3.3490.2052550.17554080.17756720.9740.98299.84130.196
3.349-3.8650.1952420.16147920.16350420.9790.98699.84130.187
3.865-4.7280.1512120.1340540.13142790.9880.9999.69620.165
4.728-6.6610.1791890.14931450.15133430.9870.9999.73080.19
6.661-55.0250.133860.14418160.14319080.9890.98999.68550.195

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