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

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Basic information

Entry
Database: PDB / ID: 1poy
TitleSPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (DIMER FORM)
ComponentsSPERMIDINE/PUTRESCINE-BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / BINDING PROTEIN
Function / homology
Function and homology information


spermidine transmembrane transport / spermidine binding / spermidine transport / putrescine transport / putrescine binding / 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: 2.5 Å
AuthorsSugiyama, S. / Vassylyev, D.G. / Matsushima, M. / Morikawa, K.
Citation
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.
#1: Journal: To be Published
Title: Crystallization and Preliminary X-Ray Analysis of the Primary Receptor (Potd) of the Polyamine Transport System in Escherichia Coli
Authors: Sugiyama, S. / Matsushima, M. / Saisho, T. / 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 1.0Jul 11, 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

Downloads & links

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Assembly

Deposited unit
1: SPERMIDINE/PUTRESCINE-BINDING PROTEIN
2: SPERMIDINE/PUTRESCINE-BINDING PROTEIN
3: SPERMIDINE/PUTRESCINE-BINDING PROTEIN
4: SPERMIDINE/PUTRESCINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,7738
Polymers145,1924
Non-polymers5814
Water4,234235
1
1: SPERMIDINE/PUTRESCINE-BINDING PROTEIN
2: SPERMIDINE/PUTRESCINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8864
Polymers72,5962
Non-polymers2902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
3: SPERMIDINE/PUTRESCINE-BINDING PROTEIN
4: SPERMIDINE/PUTRESCINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8864
Polymers72,5962
Non-polymers2902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.300, 69.100, 72.500
Angle α, β, γ (deg.)90.00, 107.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36297.879 Da / Num. of mol.: 4 / 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) / Spermidine


Mass: 145.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H19N3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.39 Å3/Da / Density % sol: 45 %
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown

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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: 2.5→300 Å / Num. obs: 38903 / % possible obs: 81.6 % / Observed criterion σ(I): 1
Reflection
*PLUS
Rmerge(I) obs: 0.0679

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
WELMSdata reduction
X-PLORphasing
RefinementResolution: 2.5→6 Å / σ(F): 1
RfactorNum. reflection
Rfree0.28 -
Rwork0.199 -
obs0.199 36198
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10240 0 40 236 10516
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.98
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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