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- PDB-6ye7: E.coli's Putrescine receptor PotF complexed with Cadaverine -

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Basic information

Entry
Database: PDB / ID: 6ye7
TitleE.coli's Putrescine receptor PotF complexed with Cadaverine
ComponentsPutrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein / E.coli / Cadaverine
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
MALONATE ION / PENTANE-1,5-DIAMINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 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: 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

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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)81,86638
Polymers78,7412
Non-polymers3,12536
Water10,809600
1
A: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,90220
Polymers39,3711
Non-polymers1,53219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,96418
Polymers39,3711
Non-polymers1,59317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.869, 70.869, 271.185
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
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 29 through 166 or resid 168...A29 - 166
121(chain 'A' and (resid 29 through 166 or resid 168...A168 - 300
131(chain 'A' and (resid 29 through 166 or resid 168...A302 - 367
141(chain 'A' and (resid 29 through 166 or resid 168...A701
151(chain 'A' and (resid 29 through 166 or resid 168...A901
161(chain 'A' and (resid 29 through 166 or resid 168...A1501
171(chain 'A' and (resid 29 through 166 or resid 168...A1601
181(chain 'A' and (resid 29 through 166 or resid 168...A1901
191(chain 'A' and (resid 29 through 166 or resid 168...A2001
1101(chain 'A' and (resid 29 through 166 or resid 168...A2101
2111(chain 'B' and (resid 29 through 166 or resid 168...B29 - 166
2121(chain 'B' and (resid 29 through 166 or resid 168...B168 - 300
2131(chain 'B' and (resid 29 through 166 or resid 168...B302 - 367
2141(chain 'B' and (resid 29 through 166 or resid 168...B701
2151(chain 'B' and (resid 29 through 166 or resid 168...B1001
2161(chain 'B' and (resid 29 through 166 or resid 168...B1301
2171(chain 'B' and (resid 29 through 166 or resid 168...B1401
2181(chain 'B' and (resid 29 through 166 or resid 168...B1701
2191(chain 'B' and (resid 29 through 166 or resid 168...B1801
2201(chain 'B' and (resid 29 through 166 or resid 168...B1901

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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 (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 , 11 types, 636 molecules

#2: Chemical ChemComp-N2P / PENTANE-1,5-DIAMINE / Cadaverine


Mass: 102.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#10: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#11: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.1 M Bicine pH 8.8, 2.4 M Ammoniumsulfate, 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: Mar 8, 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: 1.6→45.5 Å / Num. obs: 104898 / % possible obs: 99.18 % / Redundancy: 10.8 % / Biso Wilson estimate: 26.81 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09069 / Rpim(I) all: 0.02861 / Rrim(I) all: 0.09521 / Net I/σ(I): 14.85
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 9 % / Rmerge(I) obs: 2.54 / Mean I/σ(I) obs: 0.66 / Num. unique obs: 9828 / CC1/2: 0.231 / CC star: 0.612 / Rpim(I) all: 0.8662 / Rrim(I) all: 2.691 / % possible all: 94.29

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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: 1.6→45.5 Å / SU ML: 0.2083 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.2741
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2100 2 %Random selection
Rwork0.1679 ---
obs0.1684 104898 99.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5360 0 202 600 6162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00875697
X-RAY DIFFRACTIONf_angle_d0.93847663
X-RAY DIFFRACTIONf_chiral_restr0.059827
X-RAY DIFFRACTIONf_plane_restr0.007977
X-RAY DIFFRACTIONf_dihedral_angle_d18.89752107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.39631270.34656185X-RAY DIFFRACTION90.86
1.64-1.680.30941370.30426738X-RAY DIFFRACTION98.72
1.68-1.720.31231390.27726782X-RAY DIFFRACTION99.4
1.72-1.770.27361390.26086842X-RAY DIFFRACTION99.53
1.77-1.830.28311390.23186762X-RAY DIFFRACTION99.67
1.83-1.90.2321390.21386827X-RAY DIFFRACTION99.63
1.9-1.970.23461400.19246850X-RAY DIFFRACTION99.79
1.97-2.060.21051390.17266833X-RAY DIFFRACTION99.86
2.06-2.170.181400.16436864X-RAY DIFFRACTION99.96
2.17-2.310.20451410.15636894X-RAY DIFFRACTION99.93
2.31-2.480.18961410.15766908X-RAY DIFFRACTION99.86
2.48-2.730.19671420.1596939X-RAY DIFFRACTION99.86
2.73-3.130.21541420.17026973X-RAY DIFFRACTION99.79
3.13-3.940.15671440.14387051X-RAY DIFFRACTION99.92
3.94-45.50.16611510.14997350X-RAY DIFFRACTION99.48
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)
11.540995062830.286965152290.2452479120361.02477909243-0.08313324545211.10972145647-0.04833134725260.05936772493930.0901350038776-0.13534237152-0.0700431420171-0.0543752462615-0.0802316038097-0.118409725335-0.01198979813780.2087621222190.0924444081231-0.03392189931830.222320485472-0.03619151602130.19384716185-14.663599592716.8138954819-19.4954302096
22.137268742140.103588179574-0.2254682762370.924852628526-0.1564600119381.066889646680.0903389392990.4529812039680.113717948004-0.0940227186148-0.05501018515640.050527188529-0.004999638862810.0960573910108-0.005249372706310.1981393628820.106613033887-0.03511985864610.3110004271090.05033376386110.18636498163816.23781014857.07124648071-25.4783911611
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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