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- PDB-6yec: E.coli's Putrescine receptor PotF complexed with Spermine -

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Basic information

Entry
Database: PDB / ID: 6yec
TitleE.coli's Putrescine receptor PotF complexed with Spermine
ComponentsPutrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein / E.coli / Spermine
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 / SPERMINE / Putrescine-binding periplasmic protein PotF
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsShanmugaratnam, S. / Kroeger, P. / Hocker, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)HO4022/2-3 Germany
CitationJournal: Structure / Year: 2021
Title: A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF.
Authors: Kroger, P. / Shanmugaratnam, S. / Ferruz, N. / Schweimer, K. / Hocker, B.
History
DepositionMar 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,60437
Polymers78,7412
Non-polymers2,86335
Water2,558142
1
B: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,81820
Polymers39,3711
Non-polymers1,44719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,78617
Polymers39,3711
Non-polymers1,41616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.401, 70.401, 273.497
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-665-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 30 through 369 or resid 401 or resid 701 through 801 or resid 1301))A30 - 368
121(chain 'A' and (resid 30 through 369 or resid 401 or resid 701 through 801 or resid 1301))A401
131(chain 'A' and (resid 30 through 369 or resid 401 or resid 701 through 801 or resid 1301))A701
141(chain 'A' and (resid 30 through 369 or resid 401 or resid 701 through 801 or resid 1301))A801
151(chain 'A' and (resid 30 through 369 or resid 401 or resid 701 through 801 or resid 1301))A1301
261(chain 'B' and (resid 30 through 369 or resid 501 or resid 801 through 901 or resid 1301))B30 - 368
271(chain 'B' and (resid 30 through 369 or resid 501 or resid 801 through 901 or resid 1301))B501
281(chain 'B' and (resid 30 through 369 or resid 501 or resid 801 through 901 or resid 1301))B801
291(chain 'B' and (resid 30 through 369 or resid 501 or resid 801 through 901 or resid 1301))B901
2101(chain 'B' and (resid 30 through 369 or resid 501 or resid 801 through 901 or resid 1301))B1301

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Putrescine-binding periplasmic protein


Mass: 39370.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: potF, b0854, JW0838 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31133

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Non-polymers , 9 types, 177 molecules

#2: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 5% PEG 3550

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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: Jan 17, 2018
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: 2.09→45.58 Å / Num. obs: 47981 / % possible obs: 99.95 % / Redundancy: 11 % / Biso Wilson estimate: 52.43 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1083 / Rpim(I) all: 0.03414 / Rrim(I) all: 0.1137 / Net I/σ(I): 14.62
Reflection shellResolution: 2.09→2.165 Å / Redundancy: 11.4 % / Rmerge(I) obs: 3.334 / Mean I/σ(I) obs: 0.65 / Num. unique obs: 4689 / CC1/2: 0.229 / CC star: 0.61 / Rpim(I) all: 1.024 / Rrim(I) all: 3.49 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MxCuBEdata collection
XDS20180126data reduction
XDS20180126data scaling
Coot0.8.9.2model building
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A99

1a99


Resolution: 2.09→45.58 Å / SU ML: 0.3044 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.8583
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 2075 4.32 %Random selection
Rwork0.2154 45906 --
obs0.2165 47981 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.65 Å2
Refinement stepCycle: LAST / Resolution: 2.09→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5351 0 173 142 5666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00145625
X-RAY DIFFRACTIONf_angle_d0.44627594
X-RAY DIFFRACTIONf_chiral_restr0.0406823
X-RAY DIFFRACTIONf_plane_restr0.0032968
X-RAY DIFFRACTIONf_dihedral_angle_d18.01752062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.3781370.35073042X-RAY DIFFRACTION100
2.14-2.190.31021370.33013017X-RAY DIFFRACTION99.97
2.19-2.250.37571330.31862956X-RAY DIFFRACTION100
2.25-2.320.30861360.29332993X-RAY DIFFRACTION99.97
2.32-2.390.34581370.29413042X-RAY DIFFRACTION100
2.39-2.480.30051360.2793004X-RAY DIFFRACTION99.9
2.48-2.570.32111360.26553008X-RAY DIFFRACTION100
2.57-2.690.28071380.24833062X-RAY DIFFRACTION100
2.69-2.830.28511370.23823040X-RAY DIFFRACTION100
2.83-3.010.25181370.22943027X-RAY DIFFRACTION99.97
3.01-3.240.24951390.2163063X-RAY DIFFRACTION100
3.24-3.570.21541390.20323090X-RAY DIFFRACTION100
3.57-4.090.221400.18263100X-RAY DIFFRACTION100
4.09-5.150.18471420.17163135X-RAY DIFFRACTION99.85
5.15-45.580.23771510.21653327X-RAY DIFFRACTION99.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.89175769837-0.34778421023-1.69316371311.657239680890.1550460108162.97769591350.02790168596240.03901880050060.2606953065560.128980369157-0.0174222742405-0.1812328376130.378096095597-0.179603996782-0.000119983131750.6587739074980.0546147973966-0.05217717390530.362191979138-0.02703188332620.526350690584-13.9562775014-9.57698451286-65.8602900941
23.78705196094-0.2066868494270.8326564893471.70267133670.01920675477951.36709484064-0.05371813164280.00971640099893-0.0725606199210.11298080116-0.005172974040440.207307907654-0.280851086909-0.0862377446549-1.04761301679E-50.6499301791870.123858441765-0.02450338272770.3889265536790.01786062490830.430624377529-6.2755394809421.1571361321-71.7909397532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 29 through 369)
2X-RAY DIFFRACTION2(chain 'A' and resid 30 through 369)

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