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- PDB-6ye8: E.coli's Putrescine receptor PotF complexed with Spermidine -

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Basic information

Entry
Database: PDB / ID: 6ye8
TitleE.coli's Putrescine receptor PotF complexed with Spermidine
ComponentsPutrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein / E.coli / 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
(2R)-1-methoxypropan-2-amine / (2~{S})-1-(2-methoxyethoxy)propan-2-amine / SPERMIDINE / Putrescine-binding periplasmic protein PotF
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
Revision 1.3Nov 6, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,08916
Polymers78,7412
Non-polymers1,34814
Water10,791599
1
A: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9527
Polymers39,3711
Non-polymers5816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1379
Polymers39,3711
Non-polymers7668
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.830, 70.830, 272.083
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

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Components

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Protein , 1 types, 2 molecules AB

#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 K-12 (bacteria) / Gene: potF, b0854, JW0838 / Plasmid: pET21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31133

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Non-polymers , 6 types, 613 molecules

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


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-JFN / (2R)-1-methoxypropan-2-amine / jeffamine


Mass: 89.136 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H11NO
#4: Chemical ChemComp-ONT / (2~{S})-1-(2-methoxyethoxy)propan-2-amine / Jeffamine


Mass: 133.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15NO2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 10% Jeffamine M600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 13, 2018
Details: vertically collimating mirror (M1, focus at infinity)
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry and a toroidal mirror (M2)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40.71 Å / Num. obs: 128236 / % possible obs: 99.97 % / Redundancy: 11.5 % / Biso Wilson estimate: 25.35 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.07125 / Rpim(I) all: 0.02191 / Rrim(I) all: 0.07461 / Net I/σ(I): 17.79
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 11 % / Rmerge(I) obs: 2.663 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 12611 / CC1/2: 0.264 / CC star: 0.647 / Rpim(I) all: 0.8379 / Rrim(I) all: 2.794 / % possible all: 99.99

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Processing

Software
NameVersionClassification
XDS20180126data reduction
PHENIX1.17.1_3660refinement
XDS20180126data scaling
Coot0.8.9.2model building
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A99

1a99


Resolution: 1.5→40.71 Å / SU ML: 0.1903 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.9395
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 2101 1.64 %Random selection
Rwork0.1618 ---
obs0.1621 128236 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.69 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5365 0 87 599 6051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915749
X-RAY DIFFRACTIONf_angle_d1.08717840
X-RAY DIFFRACTIONf_chiral_restr0.0789866
X-RAY DIFFRACTIONf_plane_restr0.00711014
X-RAY DIFFRACTIONf_dihedral_angle_d20.53492161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.35531360.32598167X-RAY DIFFRACTION98.52
1.53-1.570.3261380.30358316X-RAY DIFFRACTION99.99
1.57-1.610.28781400.28818355X-RAY DIFFRACTION100
1.61-1.660.27161360.25678223X-RAY DIFFRACTION99.98
1.66-1.720.29721400.2378356X-RAY DIFFRACTION99.99
1.72-1.780.26771390.218349X-RAY DIFFRACTION99.96
1.78-1.850.19851380.18828302X-RAY DIFFRACTION99.98
1.85-1.930.20251400.17268399X-RAY DIFFRACTION99.99
1.93-2.030.18621390.15988362X-RAY DIFFRACTION99.96
2.03-2.160.15781400.1478396X-RAY DIFFRACTION99.99
2.16-2.330.17511400.14188394X-RAY DIFFRACTION100
2.33-2.560.17881410.14688479X-RAY DIFFRACTION100
2.56-2.930.17071410.15888503X-RAY DIFFRACTION100
2.93-3.690.16421430.14868587X-RAY DIFFRACTION99.99
3.7-40.710.16621500.14668947X-RAY DIFFRACTION99.89
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)
11.349744743420.4902139395470.1721601749671.335011691490.127594784980.619265926568-0.01508990138240.02879985830520.0848337388228-0.0405538130627-0.0355634507943-0.0796391625707-0.0860465123984-0.0718740320825-0.0001422663158580.2068823134580.05030818946760.004244557262210.204732658638-0.02807175132560.180272804321-14.470206741416.2334730794-19.6039443295
21.453420570470.492082949836-0.6758500224631.07546444317-0.1270954167751.116660126140.104690588867-0.03800467865660.2126062111040.0627324482322-0.02464635221970.08996806707930.0159988880098-0.07261650360170.01405915962910.2221478387260.02006184812340.007592576470980.14222885925-0.0354875025620.187958097655-13.6007005774-10.849644234-65.1304108043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 29 through 370)
2X-RAY DIFFRACTION2(chain 'B' and resid 29 through 368)

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