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- PDB-6ye0: E.coli's Putrescine receptor PotF complexed with Putrescine -

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Basic information

Entry
Database: PDB / ID: 6ye0
TitleE.coli's Putrescine receptor PotF complexed with Putrescine
ComponentsPutrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein / E.coli / Putrescine
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 / Chem-ONW / 1,4-DIAMINOBUTANE / Putrescine-binding periplasmic protein PotF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 2.0May 19, 2021Group: Atomic model / Data collection / Database references / Category: atom_site / citation / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.journal_volume / _citation.page_first / _citation.year / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 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
B: Putrescine-binding periplasmic protein
A: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,64210
Polymers78,7412
Non-polymers9018
Water10,269570
1
B: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8285
Polymers39,3711
Non-polymers4584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8145
Polymers39,3711
Non-polymers4444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.987, 70.987, 272.559
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:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLYSLYS(chain 'A' and (resid 29 through 30 or resid 32...AB29 - 303 - 4
12LEULEUGLUGLU(chain 'A' and (resid 29 through 30 or resid 32...AB32 - 906 - 64
13GLNGLNLEULEU(chain 'A' and (resid 29 through 30 or resid 32...AB92 - 29666 - 270
14TYRTYRVALVAL(chain 'A' and (resid 29 through 30 or resid 32...AB298 - 329272 - 303
15GLUGLUILEILE(chain 'A' and (resid 29 through 30 or resid 32...AB331 - 355305 - 329
16ARGARGARGARG(chain 'A' and (resid 29 through 30 or resid 32...AB357331
17ARGARGTHRTHR(chain 'A' and (resid 29 through 30 or resid 32...AB359 - 360333 - 334
18ALAALATHRTHR(chain 'A' and (resid 29 through 30 or resid 32...AB362 - 364336 - 338
19VALVALLYSLYS(chain 'A' and (resid 29 through 30 or resid 32...AB366 - 367340 - 341
110PUTPUTPUTPUT(chain 'A' and (resid 29 through 30 or resid 32...AG401
211GLNGLNLYSLYS(chain 'B' and (resid 29 through 30 or resid 32...BA29 - 303 - 4
212LEULEUGLUGLU(chain 'B' and (resid 29 through 30 or resid 32...BA32 - 906 - 64
213GLNGLNLEULEU(chain 'B' and (resid 29 through 30 or resid 32...BA92 - 29666 - 270
214TYRTYRVALVAL(chain 'B' and (resid 29 through 30 or resid 32...BA298 - 329272 - 303
215GLUGLUILEILE(chain 'B' and (resid 29 through 30 or resid 32...BA331 - 355305 - 329
216ARGARGARGARG(chain 'B' and (resid 29 through 30 or resid 32...BA357331
217ARGARGTHRTHR(chain 'B' and (resid 29 through 30 or resid 32...BA359 - 360333 - 334
218ALAALATHRTHR(chain 'B' and (resid 29 through 30 or resid 32...BA362 - 364336 - 338
219VALVALLYSLYS(chain 'B' and (resid 29 through 30 or resid 32...BA366 - 367340 - 341
220PUTPUTPUTPUT(chain 'B' and (resid 29 through 30 or resid 32...BC401

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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 (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 , 5 types, 578 molecules

#2: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-JFN / (2R)-1-methoxypropan-2-amine / jeffamine


Mass: 89.136 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H11NO
#4: Chemical ChemComp-ONW / (2~{R})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-amine / Jeffamine


Mass: 191.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H21NO3
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 4.5% Jeffamine M600

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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: 1.63→45.64 Å / Num. obs: 100972 / % possible obs: 99.88 % / Redundancy: 10.7 % / Biso Wilson estimate: 27.58 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1216 / Rpim(I) all: 0.03922 / Rrim(I) all: 0.1279 / Net I/σ(I): 10.07
Reflection shellResolution: 1.63→1.688 Å / Redundancy: 9.9 % / Rmerge(I) obs: 2.482 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 9934 / CC1/2: 0.274 / CC star: 0.656 / Rpim(I) all: 0.8191 / Rrim(I) all: 2.618 / % possible all: 99.81

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDS20180409data reduction
XDS20180409data scaling
PHENIX1.17.1-3660refinement
Coot0.8.9.2model building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A99

1a99


Resolution: 1.63→45.64 Å / SU ML: 0.2091 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.5131
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 2099 2.08 %Random selection
Rwork0.1722 ---
obs0.1727 100972 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.79 Å2
Refinement stepCycle: LAST / Resolution: 1.63→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5360 0 61 570 5991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01165609
X-RAY DIFFRACTIONf_angle_d0.90857626
X-RAY DIFFRACTIONf_chiral_restr0.0628842
X-RAY DIFFRACTIONf_plane_restr0.0072984
X-RAY DIFFRACTIONf_dihedral_angle_d16.41342068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.660.34591310.34626145X-RAY DIFFRACTION94.31
1.66-1.710.32421380.31176531X-RAY DIFFRACTION99.84
1.71-1.750.32551380.28526504X-RAY DIFFRACTION100
1.75-1.80.26921390.25326537X-RAY DIFFRACTION100
1.8-1.860.25661400.24036587X-RAY DIFFRACTION100
1.86-1.930.24961380.22366528X-RAY DIFFRACTION100
1.93-2.010.22291380.20536518X-RAY DIFFRACTION99.78
2.01-2.10.23011400.18596586X-RAY DIFFRACTION99.99
2.1-2.210.21891400.17746607X-RAY DIFFRACTION99.94
2.21-2.350.21461400.16726579X-RAY DIFFRACTION99.96
2.35-2.530.20851410.16636650X-RAY DIFFRACTION100
2.53-2.780.19911400.16286597X-RAY DIFFRACTION99.7
2.78-3.180.19341420.16676696X-RAY DIFFRACTION99.99
3.18-4.010.17011430.14786744X-RAY DIFFRACTION99.65
4.01-45.640.16781510.14847064X-RAY DIFFRACTION99.7
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)
12.57006189393-0.240107836437-0.2058774799391.003660203370.176158612221.050925405250.10198601397-0.4457845409180.1409206742620.0808297317873-0.0355490879607-0.1470560189960.00116053757071-0.049917002566-0.01021934275490.220019544811-0.0940747344904-0.0537549946250.279444530552-0.06178970313290.202797565845-16.2576399187.23454516654-19.9445778969
21.70751860656-0.4121582038830.3283304284091.50130421694-0.09093419600911.09597891753-0.0874085527602-0.074357545880.07015016755450.112830594083-0.07044557744760.0737889430859-0.05185331959950.147994176775-0.01200220532910.211679421354-0.0650422519852-0.02278873162680.2177442090980.03531114419770.1808419639514.513719586316.8293889425-25.907503283
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 29 through 369)

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