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

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Basic information

Entry
Database: PDB / ID: 7oyu
TitleE.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D Y87S F88Y 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 transport / putrescine binding / 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 / TRIETHYLENE GLYCOL / SPERMIDINE / Putrescine-binding periplasmic protein PotF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsShanmugaratnam, S. / Kroeger, P. / 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

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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)40,30711
Polymers39,4711
Non-polymers83610
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint32 kcal/mol
Surface area14350 Å2
Unit cell
Length a, b, c (Å)37.136, 78.606, 114.831
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: 39470.566 Da / Num. of mol.: 1 / Mutation: S38T, F88Y, A182D, D247S, 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 , 5 types, 190 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.14 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium acetate pH 4.6, 0.2 M Ammonium acetate, 30% PEG 4000

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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: Jul 11, 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: 1.95→46.36 Å / Num. obs: 25021 / % possible obs: 98.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 30.12 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.093 / Rrim(I) all: 0.227 / Net I/σ(I): 6.44
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.7 % / Rmerge(I) obs: 2.231 / Mean I/σ(I) obs: 0.79 / Num. unique obs: 14023 / CC1/2: 0.262 / CC star: 0.644 / Rpim(I) all: 0.996 / Rrim(I) all: 2.451 / % possible all: 99.2

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Processing

Software
NameVersionClassification
Coot0.9.5model building
PHENIX1.17.1_3660refinement
XDS20190315data reduction
XSCALE20190315data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A99

1a99


Resolution: 1.95→46.36 Å / SU ML: 0.2521 / Cross valid method: FREE R-VALUE / Phase error: 25.0649
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2418 1251 5 %
Rwork0.2008 23756 -
obs0.2029 25007 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.92 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2687 0 55 180 2922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472853
X-RAY DIFFRACTIONf_angle_d0.67913871
X-RAY DIFFRACTIONf_chiral_restr0.0499420
X-RAY DIFFRACTIONf_plane_restr0.0046499
X-RAY DIFFRACTIONf_dihedral_angle_d16.91891060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.030.35531350.31992581X-RAY DIFFRACTION99.23
2.03-2.120.31361390.2942626X-RAY DIFFRACTION99.64
2.12-2.230.27841360.25242601X-RAY DIFFRACTION99.56
2.23-2.370.29561370.23562590X-RAY DIFFRACTION98.7
2.37-2.560.27311360.23092589X-RAY DIFFRACTION97.85
2.56-2.810.30161380.22532624X-RAY DIFFRACTION98.33
2.81-3.220.25091400.20232657X-RAY DIFFRACTION99.93
3.22-4.060.19541430.16332713X-RAY DIFFRACTION99.96
4.06-46.360.19921470.16212775X-RAY DIFFRACTION97.34
Refinement TLS params.Method: refined / Origin x: -0.328129966486 Å / Origin y: -0.0287458903317 Å / Origin z: -11.9408554634 Å
111213212223313233
T0.230436077983 Å20.00178581252915 Å2-0.0406474099743 Å2-0.224893888424 Å2-0.0176996343893 Å2--0.26087825277 Å2
L1.38710186928 °20.196748190496 °20.0563419909884 °2-1.97623893282 °21.38546987076 °2--1.65267488129 °2
S-0.00273870482875 Å °0.104038313353 Å °-0.15709384924 Å °0.274134519822 Å °0.0427263702501 Å °-0.111313436068 Å °0.236168504827 Å °0.0395961570021 Å °0.00645561107124 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 29 through 369)

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