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

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Basic information

Entry
Database: PDB / ID: 8azb
TitleCrystal Structure of the peptide binding protein DppE from Bacillus subtilis in the unliganded state
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
Dipeptide-binding protein DppE
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 5, 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


Theoretical massNumber of molelcules
Total (without water)59,5011
Polymers59,5011
Non-polymers00
Water9,242513
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21580 Å2
Unit cell
Length a, b, c (Å)54.530, 91.080, 106.740
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 Dipeptide-binding protein DppE


Mass: 59501.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: dppE, dciAE, BSU12960 / Production host: Escherichia coli (E. coli) / References: UniProt: P26906
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Ligand free DppE was crystallised in a sitting drop formed by mixing 150 nl of the unliganded protein at 9 mg.ml-1 with 150 nl of 0.1 M MIB buffer pH 4.0, 25 % (w/v) PEG 1500.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.4→46.09 Å / Num. obs: 104801 / % possible obs: 99.6 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.026 / Rrim(I) all: 0.053 / Net I/σ(I): 20.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.67-46.056.60.0347340.9960.020.039
1.4-1.424.40.34450400.8860.2620.436

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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: 8AY0

8ay0


Resolution: 1.4→46.089 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.994 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2084 5232 4.997 %
Rwork0.1806 99479 -
all0.182 --
obs-104711 99.491 %
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: 16.093 Å2
Baniso -1Baniso -2Baniso -3
1--0.239 Å20 Å20 Å2
2---0.319 Å20 Å2
3---0.558 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4029 0 0 513 4542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124205
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163703
X-RAY DIFFRACTIONr_angle_refined_deg1.811.6495717
X-RAY DIFFRACTIONr_angle_other_deg0.5931.5678704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.791513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08710720
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.40710220
X-RAY DIFFRACTIONr_chiral_restr0.0890.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02821
X-RAY DIFFRACTIONr_nbd_refined0.2310.2731
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23464
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22059
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22168
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2309
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.217
X-RAY DIFFRACTIONr_nbd_other0.1680.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.340.233
X-RAY DIFFRACTIONr_mcbond_it1.6571.6122030
X-RAY DIFFRACTIONr_mcbond_other1.6551.6112030
X-RAY DIFFRACTIONr_mcangle_it2.4232.4242543
X-RAY DIFFRACTIONr_mcangle_other2.4252.4252544
X-RAY DIFFRACTIONr_scbond_it2.8881.8932175
X-RAY DIFFRACTIONr_scbond_other2.8831.8912174
X-RAY DIFFRACTIONr_scangle_it4.2192.7233163
X-RAY DIFFRACTIONr_scangle_other4.2182.7233164
X-RAY DIFFRACTIONr_lrange_it5.4626.0124837
X-RAY DIFFRACTIONr_lrange_other5.27923.4544699
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
1.4-1.4360.2673540.22672250.22876970.9590.96898.46690.208
1.436-1.4760.3243870.27870940.2875000.9220.94299.74670.266
1.476-1.5180.2523460.22968560.2372940.9610.96998.73870.198
1.518-1.5650.213480.18567080.18670580.9690.97799.97170.166
1.565-1.6160.2053260.16865440.1768720.9720.98299.97090.15
1.616-1.6730.1893540.15963190.16166740.9770.98499.9850.145
1.673-1.7360.2023010.16561200.16764210.9710.9821000.151
1.736-1.8070.2113320.16358660.16661990.9720.98399.98390.152
1.807-1.8870.22960.16656590.16859560.9730.98299.98320.158
1.887-1.9790.2932280.27953270.2857100.9220.93297.28550.247
1.979-2.0860.1942660.17451530.17554240.9790.98299.90780.173
2.086-2.2120.1772750.16648670.16751420.9810.9831000.169
2.212-2.3640.2732500.24145460.24348490.9340.94798.9070.22
2.364-2.5530.1692320.15142930.15245280.9830.98699.93370.161
2.553-2.7960.1922030.15839870.1641900.9770.9841000.173
2.796-3.1250.1972130.16735950.16938090.9750.98299.97370.186
3.125-3.6050.2011660.16931850.17133640.9750.98299.61360.192
3.605-4.4090.1921610.15627150.15828870.9790.98699.6190.183
4.409-6.2070.1881300.15521450.15622780.9840.98999.86830.183
6.207-46.0890.197640.17612760.17813590.980.97898.60190.211

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