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- PDB-7oyz: E.coli's putrescine receptor variant PotF/D in complex with spermidine -

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Basic information

Entry
Database: PDB / ID: 7oyz
TitleE.coli's putrescine receptor variant PotF/D 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
SPERMIDINE / Putrescine-binding periplasmic protein PotF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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
SupersessionDec 1, 2021ID: 4JDF
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 1.3Oct 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

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Assembly

Deposited unit
A: Putrescine-binding periplasmic protein PotF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7874
Polymers39,5451
Non-polymers2433
Water6,143341
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-4 kcal/mol
Surface area14360 Å2
Unit cell
Length a, b, c (Å)37.200, 81.850, 111.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Putrescine-binding periplasmic protein PotF


Mass: 39544.688 Da / Num. of mol.: 1 / Mutation: S38T, D39E, S87Y, A182D, D247S, 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
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 25% (w/v) PEG 3350, 0.1M Sodium Acetate, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0371 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 23, 2011
RadiationMonochromator: Si(111), mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0371 Å / Relative weight: 1
ReflectionResolution: 1.49→46.14 Å / Num. obs: 56881 / % possible obs: 99.98 % / Redundancy: 12.7 % / Biso Wilson estimate: 23.71 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.04 / Rrim(I) all: 0.142 / Net I/σ(I): 11.15
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 12.9 % / Rmerge(I) obs: 4.146 / Mean I/σ(I) obs: 0.58 / Num. unique obs: 71875 / CC1/2: 0.328 / CC star: 0.703 / Rpim(I) all: 1.187 / Rrim(I) all: 4.315 / % possible all: 99.96

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Processing

Software
NameVersionClassification
Coot0.9.5model building
PHENIX1.19.2_4158refinement
XDS20200417data reduction
XSCALE20200417data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A99

1a99


Resolution: 1.49→46.14 Å / SU ML: 0.2529 / Cross valid method: FREE R-VALUE / Phase error: 23.3291
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2152 2101 3.69 %
Rwork0.1756 54774 -
obs0.1771 56875 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.14 Å2
Refinement stepCycle: LAST / Resolution: 1.49→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 0 15 341 3049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242842
X-RAY DIFFRACTIONf_angle_d0.52143877
X-RAY DIFFRACTIONf_chiral_restr0.0576423
X-RAY DIFFRACTIONf_plane_restr0.0036504
X-RAY DIFFRACTIONf_dihedral_angle_d11.30611061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.520.45241290.43833352X-RAY DIFFRACTION93.55
1.52-1.560.3961390.35433632X-RAY DIFFRACTION99.92
1.56-1.60.36061380.31453603X-RAY DIFFRACTION100
1.6-1.650.3181390.26213617X-RAY DIFFRACTION100
1.65-1.70.26591390.22033629X-RAY DIFFRACTION100
1.7-1.760.25391400.19413632X-RAY DIFFRACTION99.97
1.76-1.830.25251380.18783624X-RAY DIFFRACTION99.95
1.83-1.920.26351400.20763639X-RAY DIFFRACTION100
1.92-2.020.21931400.16323644X-RAY DIFFRACTION100
2.02-2.140.2161400.15973668X-RAY DIFFRACTION99.97
2.14-2.310.21851420.15223684X-RAY DIFFRACTION100
2.31-2.540.21231400.1543665X-RAY DIFFRACTION100
2.54-2.910.21381420.16833715X-RAY DIFFRACTION100
2.91-3.660.21181440.16583739X-RAY DIFFRACTION100
3.66-46.140.17021510.16113931X-RAY DIFFRACTION99.9

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