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- PDB-1pot: SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (... -

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Basic information

Entry
Database: PDB / ID: 1pot
TitleSPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (MONOMER FORM)
ComponentsSPERMIDINE/PUTRESCINE-BINDING PROTEIN
KeywordsBINDING PROTEIN / POLYAMINE TRANSPORT PROTEIN
Function / homology
Function and homology information


spermidine transmembrane transport / spermidine binding / spermidine transport / putrescine binding / putrescine transport / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Spermidine/putrescine-binding periplasmic protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SPERMIDINE / Spermidine/putrescine-binding periplasmic protein / Spermidine/putrescine-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSugiyama, S. / Maenaka, K. / Matsushima, M. / Morikawa, K.
Citation
Journal: Protein Sci. / Year: 1996
Title: The 1.8-A X-ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding.
Authors: Sugiyama, S. / Matsuo, Y. / Maenaka, K. / Vassylyev, D.G. / Matsushima, M. / Kashiwagi, K. / Igarashi, K. / Morikawa, K.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Crystal Structure of Potd, the Primary Receptor of the Polyamine Transport System in Escherichia Coli
Authors: Sugiyama, S. / Vassylyev, D.G. / Matsushima, M. / Kashiwagi, K. / Igarashi, K. / Morikawa, K.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Functions of Pota and Potd Proteins in Spermidine-Preferential Uptake System in Escherichia Coli
Authors: Kashiwagi, K. / Miyamoto, S. / Nukui, E. / Kobayashi, H. / Igarashi, K.
History
DepositionFeb 2, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPERMIDINE/PUTRESCINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6732
Polymers36,5281
Non-polymers1451
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.300, 130.300, 38.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein SPERMIDINE/PUTRESCINE-BINDING PROTEIN / POTD


Mass: 36528.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE POLYAMINE TRANSPORT GENES IN ESCHERICHIA COLI HAD BEEN CLONED AND WAS PREVIOUSLY DESCRIBED (KASHIWAGI ET AL., (1990) J.BIOL.CHEM. 265:20893-20897, KASHIWAGI ET AL., (1991) J.BIOL.CHEM. 266:20922-20927)
Source: (natural) Escherichia coli (E. coli) / References: UniProt: P23861, UniProt: P0AFK9*PLUS
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %PEG40001drop
210 mMHEPES1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→300 Å / Num. obs: 24579 / % possible obs: 87.8 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.091
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 246531

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Processing

Software
NameClassification
PROLSQrefinement
WELMSdata reduction
RefinementResolution: 1.8→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.198 -
obs-23364
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 0 10 327 2856
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0370.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.171.5
X-RAY DIFFRACTIONp_mcangle_it1.8662
X-RAY DIFFRACTIONp_scbond_it1.5892
X-RAY DIFFRACTIONp_scangle_it2.2432.5
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1650.15
X-RAY DIFFRACTIONp_singtor_nbd0.1860.3
X-RAY DIFFRACTIONp_multtor_nbd0.2150.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2430.3
X-RAY DIFFRACTIONp_planar_tor1.83
X-RAY DIFFRACTIONp_staggered_tor22.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.198 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

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