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

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Basic information

Entry
Database: PDB / ID: 7oyw
TitleE.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D F88L S247D in complex with spermidine
ComponentsPutrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / E.coli / Periplasmic binding protein / PotF / Spermidine
Function / homology
Function and homology information


polyamine binding / polyamine transport / periplasmic space
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 / (2R)-1-methoxypropan-2-amine / (2~{S})-1-(2-methoxyethoxy)propan-2-amine / Chem-ONW / SPERMIDINE / Putrescine-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 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 20, 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

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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)80,25215
Polymers79,0492
Non-polymers1,20213
Water15,493860
1
A: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2799
Polymers39,5251
Non-polymers7548
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9736
Polymers39,5251
Non-polymers4485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.881, 71.285, 92.417
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
Components on special symmetry positions
IDModelComponents
11A-547-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putrescine-binding periplasmic protein


Mass: 39524.656 Da / Num. of mol.: 2 / Mutation: S38T, S87Y, F88L, A182D, F276W, L348Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: potF, HPE39_07830, WP7S17E04_28980 / Plasmid: pET21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6S5NLK9

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Non-polymers , 7 types, 873 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-ONT / (2~{S})-1-(2-methoxyethoxy)propan-2-amine / Jeffamine


Mass: 133.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO2
#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-3IE / (2~{S})-1-methoxypropan-2-amine


Mass: 89.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H11NO
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#7: Chemical ChemComp-JFN / (2R)-1-methoxypropan-2-amine / jeffamine


Mass: 89.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11NO
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / 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: 2.53 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.4 M AmSO4 + 0.1 M Bicine pH 9.0 + 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: Dec 11, 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: 1.28→49.39 Å / Num. obs: 198363 / % possible obs: 99.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.31 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.044 / Rrim(I) all: 0.114 / Net I/σ(I): 8.8
Reflection shellResolution: 1.28→1.33 Å / Redundancy: 6 % / Rmerge(I) obs: 2.316 / Mean I/σ(I) obs: 0.59 / Num. unique obs: 19073 / CC1/2: 0.233 / CC star: 0.615 / Rpim(I) all: 1.015 / Rrim(I) all: 2.536 / % possible all: 96.4

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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: 1.28→49.39 Å / SU ML: 0.1843 / Cross valid method: FREE R-VALUE / Phase error: 19.0846
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1613 2098 1.06 %
Rwork0.1324 196241 -
obs0.1327 198355 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.81 Å2
Refinement stepCycle: LAST / Resolution: 1.28→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5514 0 76 860 6450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086317
X-RAY DIFFRACTIONf_angle_d1.04528691
X-RAY DIFFRACTIONf_chiral_restr0.0806947
X-RAY DIFFRACTIONf_plane_restr0.01061134
X-RAY DIFFRACTIONf_dihedral_angle_d14.24172485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.310.34491330.341712414X-RAY DIFFRACTION94.99
1.31-1.340.32051390.303112985X-RAY DIFFRACTION99.61
1.34-1.380.30151390.280413039X-RAY DIFFRACTION99.87
1.38-1.420.30711390.257812998X-RAY DIFFRACTION99.76
1.42-1.460.2551390.218813076X-RAY DIFFRACTION99.8
1.46-1.510.22021390.178513068X-RAY DIFFRACTION99.82
1.51-1.580.211390.150412969X-RAY DIFFRACTION99.24
1.58-1.650.17581400.13313053X-RAY DIFFRACTION99.87
1.65-1.730.18921390.123113126X-RAY DIFFRACTION99.82
1.73-1.840.15081400.103413085X-RAY DIFFRACTION99.71
1.84-1.980.15011410.096413138X-RAY DIFFRACTION99.58
1.98-2.180.12061410.091813131X-RAY DIFFRACTION99.81
2.18-2.50.11531420.097913257X-RAY DIFFRACTION99.83
2.5-3.150.15541410.122613251X-RAY DIFFRACTION99.22
3.15-49.390.14331470.130913651X-RAY DIFFRACTION99.25

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