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

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Basic information

Entry
Database: PDB / ID: 6yed
TitleE.coli's Putrescine receptor PotF in its open apo state
ComponentsPutrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein / E.coli / open 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 K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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 23, 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)80,56527
Polymers78,7412
Non-polymers1,82425
Water5,531307
1
A: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,48717
Polymers39,3711
Non-polymers1,11616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,07910
Polymers39,3711
Non-polymers7089
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.220, 53.450, 88.130
Angle α, β, γ (deg.)90.000, 111.593, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-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 K12 (bacteria) / Gene: potF, b0854, JW0838 / Plasmid: pET21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31133

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Non-polymers , 5 types, 332 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.1 M Tris pH 7.2, 0.2 M NaCl, 35% PEG 3000

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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: Jul 12, 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: 2.18→45.9 Å / Num. obs: 67443 / % possible obs: 99.95 % / Redundancy: 10.9 % / Biso Wilson estimate: 29.95 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1565 / Rpim(I) all: 0.04914 / Rrim(I) all: 0.1642 / Net I/σ(I): 13.39
Reflection shellResolution: 2.18→2.258 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.9698 / Mean I/σ(I) obs: 4.65 / Num. unique obs: 3433 / CC1/2: 0.871 / CC star: 0.965 / Rpim(I) all: 0.3195 / Rrim(I) all: 1.023 / % possible all: 99.91

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.17.1_3660refinement
XDS20180126data reduction
XDS20180126data scaling
PHASER2.8.1phasing
XSCALE20180126data scaling
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A99

1a99


Resolution: 2.18→45.9 Å / SU ML: 0.3091 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.6271
RfactorNum. reflection% reflectionSelection details
Rfree0.273 3852 5.71 %Random selection
Rwork0.2277 ---
obs0.2303 67443 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.22 Å2
Refinement stepCycle: LAST / Resolution: 2.18→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5360 0 115 307 5782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00195613
X-RAY DIFFRACTIONf_angle_d0.49617594
X-RAY DIFFRACTIONf_chiral_restr0.0426830
X-RAY DIFFRACTIONf_plane_restr0.0034977
X-RAY DIFFRACTIONf_dihedral_angle_d16.5881776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.210.33141380.31062270X-RAY DIFFRACTION99.18
2.21-2.230.37731450.33962284X-RAY DIFFRACTION99.71
2.23-2.260.3381080.3262248X-RAY DIFFRACTION99.83
2.26-2.290.37061540.33152216X-RAY DIFFRACTION99.96
2.29-2.330.39061320.32052354X-RAY DIFFRACTION100
2.33-2.360.33411320.31362228X-RAY DIFFRACTION100
2.36-2.40.36761350.29692295X-RAY DIFFRACTION100
2.4-2.440.28811470.28032312X-RAY DIFFRACTION100
2.44-2.480.25761490.2732184X-RAY DIFFRACTION100
2.48-2.530.32041190.27372344X-RAY DIFFRACTION100
2.53-2.570.36131380.27362276X-RAY DIFFRACTION100
2.57-2.630.29391530.2882209X-RAY DIFFRACTION100
2.63-2.680.32981320.2732301X-RAY DIFFRACTION99.92
2.68-2.750.40771290.27262293X-RAY DIFFRACTION100
2.75-2.810.3081560.27362260X-RAY DIFFRACTION99.96
2.82-2.890.33581490.26052244X-RAY DIFFRACTION100
2.89-2.980.32921090.27262322X-RAY DIFFRACTION100
2.98-3.070.31911610.26362207X-RAY DIFFRACTION99.87
3.07-3.180.28581300.24972282X-RAY DIFFRACTION99.96
3.18-3.310.27961370.22112297X-RAY DIFFRACTION100
3.31-3.460.28821350.22562299X-RAY DIFFRACTION100
3.46-3.640.25811240.20662244X-RAY DIFFRACTION100
3.64-3.870.25341540.20252275X-RAY DIFFRACTION100
3.87-4.170.21331330.18442250X-RAY DIFFRACTION99.92
4.17-4.590.20321540.16242258X-RAY DIFFRACTION99.88
4.59-5.250.20081380.15232291X-RAY DIFFRACTION100
5.25-6.610.25041400.19382272X-RAY DIFFRACTION99.92
6.62-45.90.17521210.15692276X-RAY DIFFRACTION99.71
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)
11.284449899910.228726509320.06787051786672.40491124050.24263799470.483525779242-0.05787296860570.0842942422018-0.0223827322983-0.1719929029060.0412240854360.0566710485539-0.0146340179015-0.0846620990966-0.00200503807580.253157400701-0.00698924803389-0.01073437251690.105133339039-0.02423453332130.2035052800524.53223366733-11.138835131538.4120870036
20.350270942333-0.3170091297990.5464700704621.55823986256-0.5821540760810.8908492541440.0471240415878-0.2570484205830.0527940090199-0.014197258836-0.151440385495-0.198094805761-0.0652410237127-0.118025184235-0.01315576157830.2272607421540.07708485922710.0495528765610.782450095980.1466081643830.303817001688-11.3895098736-21.525457393377.0512959035
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 369)

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