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- PDB-7oyx: E.coli's putrescine receptor variant PotF/D (4JDF) with mutations... -

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Basic information

Entry
Database: PDB / ID: 7oyx
TitleE.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D Y87S F88Y S247D in complex with spermidine
ComponentsPutrescine-binding periplasmic protein PotF
KeywordsTRANSPORT PROTEIN / E.coli / Periplasmic binding protein / PotF / 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
(2~{S})-1-methoxypropan-2-amine / Chem-3IK / (2~{R})-1-(2-methoxyethoxy)propan-2-amine / Chem-4SW / (2~{S})-1-(2-methoxyethoxy)propan-2-amine / SPERMIDINE / Putrescine-binding periplasmic protein PotF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsShanmugaratnam, S. / Kroeger, P. / Hocker, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)HO4022/2-3 Germany
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Fine-tuning spermidine binding modes in the putrescine binding protein PotF.
Authors: Kroger, P. / Shanmugaratnam, S. / Scheib, U. / Hocker, B.
History
DepositionJun 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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 PotF
B: Putrescine-binding periplasmic protein PotF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,60516
Polymers78,9972
Non-polymers1,60814
Water13,799766
1
A: Putrescine-binding periplasmic protein PotF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0847
Polymers39,4991
Non-polymers5866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putrescine-binding periplasmic protein PotF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5209
Polymers39,4991
Non-polymers1,0228
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.155, 71.493, 92.661
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putrescine-binding periplasmic protein PotF


Mass: 39498.574 Da / Num. of mol.: 2 / Mutation: S38T, F88Y, A182D, F276W, L348Q
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 , 8 types, 780 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-3IE / (2~{S})-1-methoxypropan-2-amine


Mass: 89.136 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H11NO
#4: Chemical ChemComp-4SW / (2~{S})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-amine


Mass: 191.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H21NO3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#6: Chemical ChemComp-4RH / (2~{R})-1-(2-methoxyethoxy)propan-2-amine


Mass: 133.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO2
#7: Chemical ChemComp-3IK / (2~{R})-1-[(2~{R})-1-[(2~{S})-1-[(2~{S})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-yl]oxypropan-2-yl]oxypropan-2-amine


Mass: 307.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H33NO5
#8: Chemical ChemComp-ONT / (2~{S})-1-(2-methoxyethoxy)propan-2-amine / Jeffamine


Mass: 133.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 2.55 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 2.4 M AmSO4 + 0.1 M Bicine pH 8.3 + 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: Sep 26, 2019
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: 1.37→40.7 Å / Num. obs: 163742 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 16.55 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.061 / Rrim(I) all: 0.166 / Net I/σ(I): 7.21
Reflection shellResolution: 1.37→1.41 Å / Redundancy: 7.3 % / Rmerge(I) obs: 3.29 / Mean I/σ(I) obs: 0.46 / Num. unique obs: 16029 / CC1/2: 0.24 / CC star: 0.622 / Rpim(I) all: 1.295 / Rrim(I) all: 3.54 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.9.5model building
XDS20190806data reduction
XSCALE20190806data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A99

1a99


Resolution: 1.37→40.7 Å / SU ML: 0.2262 / Cross valid method: FREE R-VALUE / Phase error: 24.9749
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1933 2099 1.28 %
Rwork0.1653 161585 -
obs0.1657 163728 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.52 Å2
Refinement stepCycle: LAST / Resolution: 1.37→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 105 766 6361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01716004
X-RAY DIFFRACTIONf_angle_d1.4538211
X-RAY DIFFRACTIONf_chiral_restr0.1004897
X-RAY DIFFRACTIONf_plane_restr0.01461062
X-RAY DIFFRACTIONf_dihedral_angle_d19.54812265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.40.47391370.428510527X-RAY DIFFRACTION98.49
1.4-1.440.42021380.382610655X-RAY DIFFRACTION99.82
1.44-1.470.39251380.336110621X-RAY DIFFRACTION99.83
1.47-1.520.29671400.300810751X-RAY DIFFRACTION99.93
1.52-1.570.30661390.276410686X-RAY DIFFRACTION99.82
1.57-1.620.25321390.234910719X-RAY DIFFRACTION99.87
1.62-1.690.23251390.20910679X-RAY DIFFRACTION99.98
1.69-1.760.21941400.188810730X-RAY DIFFRACTION99.92
1.76-1.860.18861400.168810763X-RAY DIFFRACTION99.87
1.86-1.970.20551390.153110732X-RAY DIFFRACTION99.93
1.97-2.130.17241410.134210811X-RAY DIFFRACTION99.93
2.13-2.340.16391400.127110815X-RAY DIFFRACTION99.93
2.34-2.680.16681410.131910848X-RAY DIFFRACTION99.94
2.68-3.370.16921430.140110951X-RAY DIFFRACTION99.92
3.37-40.70.14921450.13611297X-RAY DIFFRACTION99.87
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)
10.600713096562-0.06273138364710.1573044203430.8114299270990.007721289369130.8137593545294.96803585467E-5-0.01415187460150.01260517055590.03240878762510.0007866295100950.0278888938703-0.02353928082190.09315787562870.0009346118320130.0616701472821-0.01473935119040.01254695852230.07603291974170.0002852279538940.098973523000711.455083642147.8128051935-17.6334614445
20.50322122677-0.06783468700850.1793721906160.6720984220480.0772436268531.40209251657-0.0145506788775-0.01100680314010.0133765661592-0.01722157573220.0275190764633-0.01205744372470.0504543573627-0.1932406494270.004569728603770.09064263465390.00195339295250.005982153110540.1380287551470.01269542016680.095007489846-16.252415770833.2369115521-59.065028623
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 29 - 401 / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 29 through 401)AA - B
22(chain 'B' and resid 29 through 401)BF - G

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