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- PDB-8ay0: Crystal Structure of the peptide binding protein DppE from Bacill... -

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Basic information

Entry
Database: PDB / ID: 8ay0
TitleCrystal Structure of the peptide binding protein DppE from Bacillus subtilis in complex with murein tripeptide
ComponentsDipeptide-binding protein DppE
KeywordsTRANSPORT PROTEIN / Peptide-binding protein / murein tripeptide / Bacillus subtilis
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / sporulation resulting in formation of a cellular spore / ATP-binding cassette (ABC) transporter complex / protein transport / periplasmic space
Similarity search - Function
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
L-ALA-GAMMA-D-GLU-MESO-DIAMINOPIMELIC ACID / Dipeptide-binding protein DppE
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsHughes, A.M. / 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
DepositionSep 1, 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: Dipeptide-binding protein DppE
B: Dipeptide-binding protein DppE
C: Dipeptide-binding protein DppE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,20033
Polymers178,5043
Non-polymers2,69630
Water21,7261206
1
A: Dipeptide-binding protein DppE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,72316
Polymers59,5011
Non-polymers1,22215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dipeptide-binding protein DppE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,27510
Polymers59,5011
Non-polymers7749
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dipeptide-binding protein DppE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2027
Polymers59,5011
Non-polymers7016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.855, 61.310, 124.073
Angle α, β, γ (deg.)78.088, 82.672, 61.597
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Dipeptide-binding protein DppE


Mass: 59501.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: dppE, dciAE, BSU12960 / Production host: Escherichia coli (E. coli) / References: UniProt: P26906
#2: Chemical ChemComp-MHI / L-ALA-GAMMA-D-GLU-MESO-DIAMINOPIMELIC ACID


Mass: 390.389 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H26N4O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1206 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Crystals of DppE suitable for X-ray analysis were obtained from hanging drops formed by mixing 1 mircol of reservoir solution containing 0.1 M Bis-Tris-Propane pH 8.5, 0.4 M MgCl2, 22.5 % ...Details: Crystals of DppE suitable for X-ray analysis were obtained from hanging drops formed by mixing 1 mircol of reservoir solution containing 0.1 M Bis-Tris-Propane pH 8.5, 0.4 M MgCl2, 22.5 % PEG 3350 and 2.5 % DMSO with 1 microl of protein at 13 mg.ml-1 .

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.51→60.74 Å / Num. obs: 233391 / % possible obs: 96.3 % / Redundancy: 2.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.053 / Rrim(I) all: 0.075 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.2 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.27-60.670.02114370.9980.0210.03
1.51-1.540.759113060.5720.7591.073

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
REFMAC5.8.0352refinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FAJ

4faj


Resolution: 1.51→60.739 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.305 / SU ML: 0.079 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2213 11490 4.923 %
Rwork0.1845 221900 -
all0.186 --
obs-233390 96.293 %
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: 24.662 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å2-0.029 Å21.355 Å2
2--0.324 Å2-2.004 Å2
3----0.326 Å2
Refinement stepCycle: LAST / Resolution: 1.51→60.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11876 0 177 1206 13259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01212365
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611001
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.65416709
X-RAY DIFFRACTIONr_angle_other_deg0.5221.56925790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69751480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.743540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.104102091
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.16910630
X-RAY DIFFRACTIONr_chiral_restr0.0790.21738
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213899
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022389
X-RAY DIFFRACTIONr_nbd_refined0.2230.22286
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.210402
X-RAY DIFFRACTIONr_nbtor_refined0.1820.25986
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.26210
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2879
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0240.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.222
X-RAY DIFFRACTIONr_nbd_other0.1790.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2780.249
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0060.21
X-RAY DIFFRACTIONr_mcbond_it2.0732.5555902
X-RAY DIFFRACTIONr_mcbond_other2.0722.5555902
X-RAY DIFFRACTIONr_mcangle_it2.8353.8257370
X-RAY DIFFRACTIONr_mcangle_other2.8353.8267371
X-RAY DIFFRACTIONr_scbond_it2.862.8216463
X-RAY DIFFRACTIONr_scbond_other2.862.8216464
X-RAY DIFFRACTIONr_scangle_it4.244.1019333
X-RAY DIFFRACTIONr_scangle_other4.244.1019334
X-RAY DIFFRACTIONr_lrange_it5.68637.88314125
X-RAY DIFFRACTIONr_lrange_other5.68537.88314125
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
1.51-1.5490.3327890.322160440.323179160.9070.91293.95510.321
1.549-1.5920.2957750.303157690.303175200.9280.92294.42920.299
1.592-1.6380.2967800.282153810.282170050.9280.93395.03680.273
1.638-1.6880.297770.267149130.269165080.9330.94295.04480.257
1.688-1.7430.2787560.251145300.252159840.9410.95195.63310.238
1.743-1.8050.2577200.226140560.228154200.9530.96195.82360.213
1.805-1.8730.2516700.216135870.218148880.9570.96695.76170.2
1.873-1.9490.2616650.205131940.208143780.9530.97196.39030.189
1.949-2.0360.2366980.197126190.199138300.9610.97496.29070.184
2.036-2.1350.2496050.19120780.193131120.9580.97796.72820.179
2.135-2.250.2256710.18115440.183125710.9660.97997.16810.172
2.25-2.3860.2085530.171109360.173118110.9710.98197.27370.166
2.386-2.5510.2115320.163103220.165111230.970.98397.58160.16
2.551-2.7550.2065640.16295980.165103640.9730.98498.05090.162
2.755-3.0170.2174500.16788750.1794910.9710.98298.2510.172
3.017-3.3720.2094220.16980870.17186490.9730.98398.38130.178
3.372-3.8920.2033900.16270710.16475590.9750.98598.70350.179
3.892-4.7620.173540.13660070.13864440.9840.98998.7120.16
4.762-6.7130.1932090.16647060.16749680.9820.98898.93320.192
6.713-60.7390.1941100.16425840.16527550.9810.98297.78580.197

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