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

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Basic information

Entry
Database: PDB / ID: 7oyt
TitleE.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D F88L 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
ACETATE ION / 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: 1.6 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
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)41,33826
Polymers39,4971
Non-polymers1,84225
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint56 kcal/mol
Surface area14410 Å2
Unit cell
Length a, b, c (Å)37.135, 78.028, 118.444
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: 39496.645 Da / Num. of mol.: 1 / Mutation: S38T, S87Y, F88L, 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 , 8 types, 236 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.26 Å3/Da / Density % sol: 43.38 %
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: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 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: 1.6→39.01 Å / Num. obs: 46390 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.16 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.054 / Rrim(I) all: 0.139 / Net I/σ(I): 9.03
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 6.2 % / Rmerge(I) obs: 2.421 / Mean I/σ(I) obs: 0.66 / Num. unique obs: 26997 / CC1/2: 0.273 / CC star: 0.655 / Rpim(I) all: 1.051 / Rrim(I) all: 2.645 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Coot0.9.5model building
PHENIX1.17.1_3660refinement
XDS20190806data reduction
XSCALE20190806data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A99

1a99


Resolution: 1.6→39.01 Å / SU ML: 0.238 / Cross valid method: FREE R-VALUE / Phase error: 23.6974
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2092 2100 4.53 %
Rwork0.1777 44290 -
obs0.1791 46390 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.39 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2689 0 119 211 3019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112908
X-RAY DIFFRACTIONf_angle_d1.04643907
X-RAY DIFFRACTIONf_chiral_restr0.0736420
X-RAY DIFFRACTIONf_plane_restr0.0078497
X-RAY DIFFRACTIONf_dihedral_angle_d18.11941081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.39731350.36192839X-RAY DIFFRACTION97.96
1.64-1.680.35891380.34412901X-RAY DIFFRACTION99.7
1.68-1.720.33651380.32182914X-RAY DIFFRACTION99.87
1.72-1.770.33931390.28432945X-RAY DIFFRACTION99.94
1.77-1.830.28691370.25042889X-RAY DIFFRACTION99.8
1.83-1.890.31151390.22732920X-RAY DIFFRACTION100
1.89-1.970.25271400.20552945X-RAY DIFFRACTION99.87
1.97-2.060.22791390.17852949X-RAY DIFFRACTION99.58
2.06-2.170.2261390.16472923X-RAY DIFFRACTION100
2.17-2.30.19191390.15982942X-RAY DIFFRACTION99.9
2.3-2.480.21921410.15722965X-RAY DIFFRACTION99.78
2.48-2.730.22161400.15992952X-RAY DIFFRACTION99.84
2.73-3.130.18211430.15453007X-RAY DIFFRACTION99.87
3.13-3.940.20371430.1473017X-RAY DIFFRACTION99.72
3.94-39.010.14421500.16663182X-RAY DIFFRACTION99.61
Refinement TLS params.Method: refined / Origin x: -0.807947340349 Å / Origin y: 0.00105818381567 Å / Origin z: -12.4409711457 Å
111213212223313233
T0.154329462058 Å20.0121202430783 Å2-0.0259780356158 Å2-0.164201500396 Å20.00159172024974 Å2--0.18084873856 Å2
L0.845014277172 °2-0.0324007754102 °2-0.189836470615 °2-1.41900290404 °20.969852474184 °2--1.36316589918 °2
S-0.000539268229945 Å °-0.0159579546209 Å °-0.10625757383 Å °0.168581947953 Å °-0.00272259107948 Å °-0.0235370426623 Å °0.178347212759 Å °0.0504559080906 Å °0.0026210596441 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 29 through 369)

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