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- PDB-7oyy: E.coli's putrescine receptor variant PotF/D (4JDF) with mutation ... -

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Basic information

Entry
Database: PDB / ID: 7oyy
TitleE.coli's putrescine receptor variant PotF/D (4JDF) with mutation S247D in complex with spermidine
ComponentsPutrescine-binding periplasmic protein PotF
KeywordsTRANSPORT PROTEIN / E.coli / Periplasmic binding protein / PotF / Spermidine
Function / homology
Function and homology information


putrescine binding / putrescine transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Spermidine/putrescine-binding periplasmic protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / SPERMIDINE / Putrescine-binding periplasmic protein PotF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsKroeger, P. / Shanmugaratnam, S. / Hocker, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)HO4022/2-3 Germany
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Fine-tuning spermidine binding modes in the putrescine binding protein PotF.
Authors: Kroger, P. / Shanmugaratnam, S. / Scheib, U. / Hocker, B.
History
DepositionJun 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putrescine-binding periplasmic protein PotF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1388
Polymers39,5731
Non-polymers5657
Water9,314517
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint5 kcal/mol
Surface area14700 Å2
Unit cell
Length a, b, c (Å)37.059, 82.146, 111.071
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putrescine-binding periplasmic protein PotF


Mass: 39572.695 Da / Num. of mol.: 1 / Mutation: S38T, D39E, S87Y, A182D, F276W, L348Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: potF, b0854, JW0838 / Plasmid: pET21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31133

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Non-polymers , 6 types, 524 molecules

#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M MES pH 5, 30% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 7, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.36→35.15 Å / Num. obs: 73425 / % possible obs: 99.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 14.51 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.068 / Rrim(I) all: 0.184 / Net I/σ(I): 7.58
Reflection shellResolution: 1.36→1.41 Å / Redundancy: 7.3 % / Rmerge(I) obs: 2.53 / Mean I/σ(I) obs: 0.61 / Num. unique obs: 52254 / CC1/2: 0.28 / CC star: 0.661 / Rpim(I) all: 0.988 / Rrim(I) all: 2.721 / % possible all: 98

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Processing

Software
NameVersionClassification
Coot0.9.5model building
PHENIX1.19.2_4158refinement
XDS20190806data reduction
XSCALE20190806data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A99

1a99


Resolution: 1.36→35.15 Å / SU ML: 0.1875 / Cross valid method: FREE R-VALUE / Phase error: 19.7446
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1859 2100 2.86 %
Rwork0.1563 71315 -
obs0.1571 73415 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.66 Å2
Refinement stepCycle: LAST / Resolution: 1.36→35.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 36 517 3257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682986
X-RAY DIFFRACTIONf_angle_d0.91174080
X-RAY DIFFRACTIONf_chiral_restr0.0762444
X-RAY DIFFRACTIONf_plane_restr0.0071531
X-RAY DIFFRACTIONf_dihedral_angle_d12.70461150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.390.36651340.33354555X-RAY DIFFRACTION96.18
1.39-1.430.32821380.29514670X-RAY DIFFRACTION98.61
1.43-1.460.30731380.26654673X-RAY DIFFRACTION99.94
1.46-1.510.27211370.2374668X-RAY DIFFRACTION98.99
1.51-1.560.25411390.22984732X-RAY DIFFRACTION99.29
1.56-1.610.24331400.20594736X-RAY DIFFRACTION99.51
1.61-1.680.24051380.184706X-RAY DIFFRACTION99.98
1.68-1.750.21441390.16484723X-RAY DIFFRACTION99.67
1.75-1.850.17241400.14554759X-RAY DIFFRACTION99.8
1.85-1.960.18251410.13844768X-RAY DIFFRACTION99.88
1.96-2.110.19161400.13514755X-RAY DIFFRACTION99.94
2.11-2.320.16361410.12314801X-RAY DIFFRACTION99.9
2.32-2.660.16381430.1314851X-RAY DIFFRACTION100
2.66-3.350.16721430.1334872X-RAY DIFFRACTION99.98
3.35-35.150.14531490.14545046X-RAY DIFFRACTION99.25

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