6ye7

E.coli's Putrescine receptor PotF complexed with Cadaverine

Method: X-RAY DIFFRACTION D_max: 79.2 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Putrescine-binding periplasmic protein

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 27–370	Not recorded	N2P PENTANE-1,5-DIAMINE × 1 EDO 1,2-ETHANEDIOL × 12 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；0.1 M Bicine pH 8.8, 2.4 M Ammoniumsulfate, 5% PEG 3550	Resolution 1.60 Å R-free 0.194
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 27–370	Not recorded	N2P PENTANE-1,5-DIAMINE × 1 EDO 1,2-ETHANEDIOL × 11 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 MLI MALONATE ION × 1 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；0.1 M Bicine pH 8.8, 2.4 M Ammoniumsulfate, 5% PEG 3550	Resolution 1.60 Å R-free 0.194

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6YE7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A99 PUTRESCINE RECEPTOR (POTF) FROM E. COLI Deposited 1998-04-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–370（344 aa）	Not recorded	PUT 1,4-DIAMINOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；PROTEIN WAS CRYSTALLIZED FROM 2M AMMONIUM SULFATE, 6% GLYCEROL, 200MM CACODYLATE BUFFER (PH 5), pH 5.0	Resolution 2.20 Å R-free 0.233
1A99 PUTRESCINE RECEPTOR (POTF) FROM E. COLI Deposited 1998-04-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–370（344 aa）	Not recorded	PUT 1,4-DIAMINOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；PROTEIN WAS CRYSTALLIZED FROM 2M AMMONIUM SULFATE, 6% GLYCEROL, 200MM CACODYLATE BUFFER (PH 5), pH 5.0	Resolution 2.20 Å R-free 0.233
1A99 PUTRESCINE RECEPTOR (POTF) FROM E. COLI Deposited 1998-04-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 27–370（344 aa）	Not recorded	PUT 1,4-DIAMINOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；PROTEIN WAS CRYSTALLIZED FROM 2M AMMONIUM SULFATE, 6% GLYCEROL, 200MM CACODYLATE BUFFER (PH 5), pH 5.0	Resolution 2.20 Å R-free 0.233
1A99 PUTRESCINE RECEPTOR (POTF) FROM E. COLI Deposited 1998-04-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 27–370（344 aa）	Not recorded	PUT 1,4-DIAMINOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；PROTEIN WAS CRYSTALLIZED FROM 2M AMMONIUM SULFATE, 6% GLYCEROL, 200MM CACODYLATE BUFFER (PH 5), pH 5.0	Resolution 2.20 Å R-free 0.233
6YE0 E.coli's Putrescine receptor PotF complexed with Putrescine Deposited 2020-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–370（344 aa）	Not recorded	PUT 1,4-DIAMINOBUTANE × 1 JFN (2R)-1-methoxypropan-2-amine × 2 ONW (2~{R})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 4.5% Jeffamine M600	Resolution 1.63 Å R-free 0.200
6YE0 E.coli's Putrescine receptor PotF complexed with Putrescine Deposited 2020-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–370（344 aa）	Not recorded	PUT 1,4-DIAMINOBUTANE × 1 JFN (2R)-1-methoxypropan-2-amine × 1 ONT (2~{S})-1-(2-methoxyethoxy)propan-2-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 4.5% Jeffamine M600	Resolution 1.63 Å R-free 0.200
6YE6 E.coli's Putrescine receptor PotF complexed with Agmatine Deposited 2020-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–370（344 aa）	Not recorded	ONT (2~{S})-1-(2-methoxyethoxy)propan-2-amine × 2 JFN (2R)-1-methoxypropan-2-amine × 7 AG2 AGMATINE × 1 ONW (2~{R})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-amine × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 7% Jeffamine M600	Resolution 1.56 Å R-free 0.185
6YE6 E.coli's Putrescine receptor PotF complexed with Agmatine Deposited 2020-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–370（344 aa）	Not recorded	ONT (2~{S})-1-(2-methoxyethoxy)propan-2-amine × 2 JFN (2R)-1-methoxypropan-2-amine × 8 AG2 AGMATINE × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 7% Jeffamine M600	Resolution 1.56 Å R-free 0.185
6YE8 E.coli's Putrescine receptor PotF complexed with Spermidine Deposited 2020-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–370（344 aa）	Not recorded	SPD SPERMIDINE × 1 JFN (2R)-1-methoxypropan-2-amine × 3 ONT (2~{S})-1-(2-methoxyethoxy)propan-2-amine × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 10% Jeffamine M600	Resolution 1.50 Å R-free 0.183
6YE8 E.coli's Putrescine receptor PotF complexed with Spermidine Deposited 2020-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–370（344 aa）	Not recorded	SPD SPERMIDINE × 1 JFN (2R)-1-methoxypropan-2-amine × 4 ONT (2~{S})-1-(2-methoxyethoxy)propan-2-amine × 1 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 10% Jeffamine M600	Resolution 1.50 Å R-free 0.183
6YEB E.coli's Putrescine receptor PotF in its closed apo state Deposited 2020-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–370（344 aa）	Not recorded	GOL GLYCEROL × 1 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 7 SO4 SULFATE ION × 2 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 5% PEG 3550	Resolution 1.97 Å R-free 0.219
6YEB E.coli's Putrescine receptor PotF in its closed apo state Deposited 2020-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–370（344 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 5 EDO 1,2-ETHANEDIOL × 10 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 5% PEG 3550	Resolution 1.97 Å R-free 0.219
6YEC E.coli's Putrescine receptor PotF complexed with Spermine Deposited 2020-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–370（344 aa）	Not recorded	SPM SPERMINE × 1 EDO 1,2-ETHANEDIOL × 9 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 5% PEG 3550	Resolution 2.09 Å R-free 0.240
6YEC E.coli's Putrescine receptor PotF complexed with Spermine Deposited 2020-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–370（344 aa）	Not recorded	SPM SPERMINE × 1 EDO 1,2-ETHANEDIOL × 6 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1 SO4 SULFATE ION × 2 CL CHLORIDE ION × 3 GOL GLYCEROL × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；2.4 M Ammoniumsulfate, 0.1 M Bicine pH 8.8, 5% PEG 3550	Resolution 2.09 Å R-free 0.240
6YED E.coli's Putrescine receptor PotF in its open apo state Deposited 2020-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–370（344 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 11 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；0.1 M Tris pH 7.2, 0.2 M NaCl, 35% PEG 3000	Resolution 2.18 Å R-free 0.273
6YED E.coli's Putrescine receptor PotF in its open apo state Deposited 2020-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–370（344 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 4 EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；0.1 M Tris pH 7.2, 0.2 M NaCl, 35% PEG 3000	Resolution 2.18 Å R-free 0.273
7OYT E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D F88L in complex with spermidine Deposited 2021-06-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–370（344 aa）	Mutation：S38T, S87Y, F88L, A182D, D247S, F276W, L348Q	SPD SPERMIDINE × 1 GOL GLYCEROL × 2 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 17 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M Sodium acetate pH 4.6, 0.2 M Ammonium acetate, 30% PEG 4000	Resolution 1.60 Å R-free 0.209
7OYU E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D Y87S F88Y in complex with spermidine Deposited 2021-06-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–370（344 aa）	Mutation：S38T, F88Y, A182D, D247S, F276W, L348Q	PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 7 PEG DI(HYDROXYETHYL)ETHER × 1 SPD SPERMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M Sodium acetate pH 4.6, 0.2 M Ammonium acetate, 30% PEG 4000	Resolution 1.95 Å R-free 0.242
7OYX E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D Y87S F88Y S247D in complex with spermidine Deposited 2021-06-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–370（344 aa）	Mutation：S38T, F88Y, A182D, F276W, L348Q	SPD SPERMIDINE × 1 3IE (2~{S})-1-methoxypropan-2-amine × 2 4SW (2~{S})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-amine × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；293 K；2.4 M AmSO4 + 0.1 M Bicine pH 8.3 + 4.5% Jeffamine M600	Resolution 1.37 Å R-free 0.193
7OYX E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D Y87S F88Y S247D in complex with spermidine Deposited 2021-06-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–370（344 aa）	Mutation：S38T, F88Y, A182D, F276W, L348Q	SPD SPERMIDINE × 1 3IE (2~{S})-1-methoxypropan-2-amine × 3 CL CHLORIDE ION × 1 4RH (2~{R})-1-(2-methoxyethoxy)propan-2-amine × 1 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 × 1 ONT (2~{S})-1-(2-methoxyethoxy)propan-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；293 K；2.4 M AmSO4 + 0.1 M Bicine pH 8.3 + 4.5% Jeffamine M600	Resolution 1.37 Å R-free 0.193
7OYY E.coli's putrescine receptor variant PotF/D (4JDF) with mutation S247D in complex with spermidine Deposited 2021-06-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–370（344 aa）	Mutation：S38T, D39E, S87Y, A182D, F276W, L348Q	SPD SPERMIDINE × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；0.1 M MES pH 5, 30% PEG 6000	Resolution 1.36 Å R-free 0.186
7OYZ E.coli's putrescine receptor variant PotF/D in complex with spermidine Deposited 2021-06-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–370（344 aa）	Mutation：S38T, D39E, S87Y, A182D, D247S, F276W, L348Q	SPD SPERMIDINE × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；25% (w/v) PEG 3350, 0.1M Sodium Acetate, pH 4.5	Resolution 1.49 Å R-free 0.215
8ASZ PotF with mutations S87Y and A182D in complex with Agmatine Deposited 2022-08-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–370（344 aa）	Mutation：S87Y, A182D	AG2 AGMATINE × 1 EDO 1,2-ETHANEDIOL × 10 GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.17 M AmAcetate, 0.085 M NaAcetate pH 4.6, 30% PEG 4000, 15% Glycerol	Resolution 1.28 Å R-free 0.209
8AT0 PotF with mutation D247K Deposited 2022-08-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–370（342 aa）	Mutation：D247K	ONT (2~{S})-1-(2-methoxyethoxy)propan-2-amine × 2 SO4 SULFATE ION × 2 JFN (2R)-1-methoxypropan-2-amine × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；2.4 M AmSO4, 0.1 M Bicine pH 9, 10% Jeffamine M600 pH7.0	Resolution 2.00 Å R-free 0.243
8AT0 PotF with mutation D247K Deposited 2022-08-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–370（342 aa）	Mutation：D247K	ONT (2~{S})-1-(2-methoxyethoxy)propan-2-amine × 1 SO4 SULFATE ION × 2 JFN (2R)-1-methoxypropan-2-amine × 1 MLI MALONATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；2.4 M AmSO4, 0.1 M Bicine pH 9, 10% Jeffamine M600 pH7.0	Resolution 2.00 Å R-free 0.243

14 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POTF_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–344； UniProt 27–370 Author chain B； PDBConstruct 1–344； UniProt 27–370

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6ye7
Deposition date deposition_date	2020-03-24
Structure title title	E.coli's Putrescine receptor PotF complexed with Cadaverine
Keywords keywords	Periplasmic binding protein, E.coli, Cadaverine, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.05 Å
Radius of gyration Rg (electron density) rg_electron	25.87 Å
Forward intensity I(0) i0	94594600.00
Molecular weight molecular_weight	78931.0 kDa
Excluded volume excluded_volume	99870 Å³
Envelope volume envelope_volume	116190 Å³
Hydration-shell volume shell_volume	35736 Å³
Envelope diameter envelope_diameter	80.6 Å
Shell Rg shell_rg	34.70 Å
Envelope Rg envelope_rg	25.79 Å
Shape Rg shape_rg	25.82 Å
Total Rg total_rg	26.93 Å
Total atoms total_atoms	11145
Residues n_residues	682
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	79.2 Å
Rg (real space) rg_real	26.86 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	9.4590e+07
I(0) uncertainty (real space) i0_real_error	1.2090e+06
Rg (reciprocal space) rg_reciprocal	26.92 Å
I(0) (reciprocal space) i0_reciprocal	94600000.0000
Solution quality estimate total_estimate	0.9111
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.9 Å
Skewness Skewness skewness	0.098
Kurtosis Kurtosis kurtosis	-0.569
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23970000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.974; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.933

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Description description	Putrescine-binding periplasmic protein
Molecular weight formula_weight	39370.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11830

AEQKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHDPDNKFAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPEEVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGWAGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAKNKDEAYQFLNYLLRPDVVAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWTKVKSGKLEHHHHHH

来源 Source

来源生物 organism	Escherichia coli (strain K12)
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PENTANE-1,5-DIAMINE
Molecular weight formula_weight	102.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	23

Entity 4 Entity 4 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	TRIS(HYDROXYETHYL)AMINOMETHANE
Molecular weight formula_weight	163.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
Molecular weight formula_weight	326.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	600

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6ye7a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d6ye7b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

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8. Citations (1)

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Unit-cell length a length_a	70.869 Å
Unit-cell length b length_b	70.869 Å
Unit-cell length c length_c	271.185 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	trigonal

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	45.500 Å
R factor r_factor	0.1684
R_work r_work	0.1679
R_free r_free	0.1940

fit	/app/data/saxs_computation/ye/6ye7/6ye7.fit
pddf	/app/data/pr_computation/ye/6ye7/6ye7.pr.out
profile	/app/data/saxs_computation/ye/6ye7/6ye7.dat