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- PDB-6yeb: E.coli's Putrescine receptor PotF in its closed apo state -

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Basic information

Entry
Database: PDB / ID: 6yeb
TitleE.coli's Putrescine receptor PotF in its closed apo state
ComponentsPutrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein / E.coli / closed apo
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 / TRIETHYLENE GLYCOL / Putrescine-binding periplasmic protein PotF
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 1.3Oct 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

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)81,07033
Polymers78,7412
Non-polymers2,32931
Water4,666259
1
A: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,45216
Polymers39,3711
Non-polymers1,08115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,61817
Polymers39,3711
Non-polymers1,24716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.118, 71.118, 272.420
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 , 7 types, 290 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.53 Å3/Da / Density % sol: 51.3 %
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: 1.97→45.68 Å / Num. obs: 58117 / % possible obs: 99.95 % / Redundancy: 10.9 % / Biso Wilson estimate: 44.59 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1242 / Rpim(I) all: 0.0393 / Rrim(I) all: 0.1304 / Net I/σ(I): 12.16
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 11.3 % / Rmerge(I) obs: 3.324 / Mean I/σ(I) obs: 0.68 / Num. unique obs: 5691 / CC1/2: 0.23 / CC star: 0.611 / Rpim(I) all: 1.021 / Rrim(I) all: 3.48 / % possible all: 99.93

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Processing

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

1a99


Resolution: 1.97→45.68 Å / SU ML: 0.2248 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6066
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 2009 3.46 %Random selection
Rwork0.1907 ---
obs0.1916 58117 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.64 Å2
Refinement stepCycle: LAST / Resolution: 1.97→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5356 0 144 259 5759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00895625
X-RAY DIFFRACTIONf_angle_d0.93397600
X-RAY DIFFRACTIONf_chiral_restr0.0582827
X-RAY DIFFRACTIONf_plane_restr0.0076973
X-RAY DIFFRACTIONf_dihedral_angle_d19.92422059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.29711370.32623882X-RAY DIFFRACTION98.48
2.02-2.070.33721420.31023945X-RAY DIFFRACTION100
2.07-2.130.34171420.28983933X-RAY DIFFRACTION100
2.13-2.20.33411430.2773978X-RAY DIFFRACTION100
2.2-2.280.29631430.24583951X-RAY DIFFRACTION99.95
2.28-2.370.27211440.23643997X-RAY DIFFRACTION100
2.37-2.480.24961400.21833939X-RAY DIFFRACTION100
2.48-2.610.25411450.19963980X-RAY DIFFRACTION100
2.61-2.770.24261410.19673963X-RAY DIFFRACTION99.93
2.77-2.980.21441470.1944041X-RAY DIFFRACTION100
2.99-3.280.22211410.17923999X-RAY DIFFRACTION100
3.29-3.760.1821470.16724075X-RAY DIFFRACTION99.98
3.76-4.740.18431480.14914123X-RAY DIFFRACTION100
4.74-45.680.20621490.19244302X-RAY DIFFRACTION99.84
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)
12.238594182340.3960568885670.5880180656722.037377561640.4022686736931.66913808526-0.0670389148789-0.0308998624120.08821520289680.128569065703-0.154895484760.214755907094-0.372566986971-0.0683744022067-0.01060804352920.556343467980.0643293244059-0.07000569726580.2851484542790.03219148243540.381988476353-7.0587719237521.5273070609-71.1853967049
21.632224935910.428244379423-0.8371654758011.93868158759-0.2702264937652.68041192568-0.00757636882867-0.1155195128780.09225326452710.306640880232-0.0938635364447-0.04347643691590.332519285974-0.100466775243-0.002695377850490.5817438636930.003982685847670.0116220883140.272472294578-0.0512180754350.390334242064-14.1497753811-10.0762223992-65.3911179264
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 29 through 369)
2X-RAY DIFFRACTION2(chain 'B' and resid 29 through 368)

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