SAXSdb — 9fxe

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

Purine nucleoside phosphorylase DeoD-type

Escherichia coli K-12

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–239 Chain B； UniProt 1–239 Chain C； UniProt 1–239	Not recorded	PO4 PHOSPHATE ION × 6 A1IEC N,2,3-etheno-2-aminopurine × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；Citrate buffer pH 5.2, amonium sulphate 24% w/v	Resolution 2.12 Å R-free 0.233

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 9FXE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A69 PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX WITH FORMYCIN B AND SULPHATE (PHOSPHATE) Deposited 1998-03-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa）	Not recorded	SO4 SULFATE ION × 6 FMB FORMYCIN B × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.3；28-35% AMMONIUM SULPHATE, 50 MM CITRATE BUFFER, PH 5.2-5.4, pH 5.3	Resolution 2.10 Å
1ECP PURINE NUCLEOSIDE PHOSPHORYLASE Deposited 1995-07-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa） Chain D 1–238（238 aa） Chain E 1–238（238 aa） Chain F 1–238（238 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.290
1K9S PURINE NUCLEOSIDE PHOSPHORYLASE FROM E. COLI IN COMPLEX WITH FORMYCIN A DERIVATIVE AND PHOSPHATE Deposited 2001-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–237（237 aa） Chain B 1–237（237 aa） Chain C 1–237（237 aa） Chain D 1–237（237 aa） Chain E 1–237（237 aa） Chain F 1–237（237 aa）	Not recorded	PO4 PHOSPHATE ION × 6 FM2 2-(7-AMINO-6-METHYL-3H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL × 3 FM1 2-HYDROXYMETHYL-5-(7-METHYLAMINO-3H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-TETRAHYDRO-FURAN-3,4-DIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；28-35% ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.184
1OTX Purine Nucleoside Phosphorylase M64V mutant Deposited 2003-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa）	Mutation：M64V Mutation：M64V Mutation：M64V	PO4 PHOSPHATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50mM sodium citrate, 30%ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.247
1OTY Native PNP +ALLO Deposited 2003-03-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa）	Not recorded	PO4 PHOSPHATE ION × 6 6MP 6-METHYLPURINE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50mM sodium citrate, 30% ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.236
1OU4 Native PNP +Talo Deposited 2003-03-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa）	Not recorded	PO4 PHOSPHATE ION × 6 6MP 6-METHYLPURINE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50mM sodium Citrate, 30% ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.244
1OUM M64V PNP +Talo Deposited 2003-03-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa）	Mutation：M64V Mutation：M64V Mutation：M64V	TAL 9-(6-DEOXY-ALPHA-L-TALOFURANOSYL)-6-METHYLPURINE × 6 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50mM sodium citrate, 30% ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.40 Å R-free 0.260
1OV6 M64V PNP + ALLO Deposited 2003-03-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Fragment：Purine Nuleoside Phosphorylase Chain B 1–238（238 aa） Fragment：Purine Nuleoside Phosphorylase Chain C 1–238（238 aa） Fragment：Purine Nuleoside Phosphorylase	Mutation：M64V Mutation：M64V Mutation：M64V	PO4 PHOSPHATE ION × 6 DBM 9-(6-DEOXY-BETA-D-ALLOFURANOSYL)-6-METHYLPURINE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50mM sodium citrate, 30% ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.40 Å R-free 0.258
1OVG M64V PNP +MePdr Deposited 2003-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–238（238 aa） Chain B 1–238（238 aa） Chain C 1–238（238 aa）	Mutation：M64V Mutation：M64V Mutation：M64V	PO4 PHOSPHATE ION × 6 MDR 9-(2-DEOXY-BETA-D-RIBOFURANOSYL)-6-METHYLPURINE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50mM sodium citrate, 30% ammonium sulfate , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.259
3UT6 Crystal structure of E. Coli PNP complexed with PO4 and formycin A Deposited 2011-11-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–238（237 aa） Chain B 2–238（237 aa） Chain C 2–238（237 aa）	Not recorded	FMC (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol × 6 PO4 PHOSPHATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 5.2；291 K；50mM citrate buffer, 35% ammonium phosphate (w/v), pH 5.2, hanging drop, temperature 291K	Resolution 1.90 Å R-free 0.187
4TTI Crystal structure of double mutant E. Coli purine nucleoside phosphorylase with 4 FMC molecules Deposited 2014-06-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: Hexameric	Chain A 2–238（237 aa） Chain B 2–238（237 aa） Chain C 2–238（237 aa） Chain D 2–238（237 aa） Chain E 2–238（237 aa） Chain F 2–238（237 aa）	Not recorded	FMC (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol × 4 PO4 PHOSPHATE ION × 6 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；50 mM citric buffer, 34 % ammonium sulphate	Resolution 1.89 Å R-free 0.210
4TTJ Crystal structure of double mutant E. Coli purine nucleoside phosphorylase with 6 FMC molecules Deposited 2014-06-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: Hexameric	Chain A 2–238（237 aa） Chain B 2–238（237 aa） Chain D 2–238（237 aa）	Not recorded	PO4 PHOSPHATE ION × 6 FMC (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol × 6 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；50 mM citric buffer, 32 % ammonium sulphate	Resolution 1.87 Å R-free 0.194
5IU6 Crystal structure of E.coli purine nucleoside phosphorylase with 7-deazahypoxanthine Deposited 2016-03-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–238（237 aa） Chain B 2–238（237 aa） Chain C 2–238（237 aa）	Not recorded	7HX 7H-pyrrolo[2,3-d]pyrimidin-4-ol × 6 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；294 K；AMMONIUM SULPHATE	Resolution 2.51 Å R-free 0.200
6XZ2 Crystal structure of E. Coli purine nucleoside phosphorylase mutant Y160W with SO4 and Formycin A Deposited 2020-01-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 2–238（237 aa） Chain B 2–238（237 aa） Chain C 2–238（237 aa）	Mutation：Y160W Mutation：Y160W Mutation：Y160W	SO4 SULFATE ION × 6 FMC (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；50 mM citrate buffer pH 5.2, 14 % ammonium sulphate (w/v)	Resolution 1.65 Å R-free 0.192
6XZ2 Crystal structure of E. Coli purine nucleoside phosphorylase mutant Y160W with SO4 and Formycin A Deposited 2020-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–238（237 aa） Chain B 2–238（237 aa） Chain C 2–238（237 aa）	Mutation：Y160W Mutation：Y160W Mutation：Y160W	SO4 SULFATE ION × 3 FMC (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；50 mM citrate buffer pH 5.2, 14 % ammonium sulphate (w/v)	Resolution 1.65 Å R-free 0.192
9FPE Wild type Purine Nucleoside Phosphorylase from E.coli in complex with N2,3-etheno-2-aminopurine Deposited 2024-06-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–239（239 aa） Chain B 1–239（239 aa） Chain C 1–239（239 aa）	Not recorded	GOL GLYCEROL × 6 A1IEC N,2,3-etheno-2-aminopurine × 6 PO4 PHOSPHATE ION × 6 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；291 K；Citrate buffer pH 5.2, amonium sulphate 15% w/v	Resolution 1.35 Å R-free 0.213

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DEOD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–239； UniProt 1–239 Author chain B； PDBConstruct 1–239； UniProt 1–239 Author chain C； PDBConstruct 1–239； UniProt 1–239

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9fxe
Deposition date deposition_date	2024-07-01
最后修订 last_revision	2024-10-30
Structure title title	D204N mutant of Purine Nucleoside Phosphorylase from E.coli in complex with N2,3-etheno-2-aminopurine
Keywords keywords	fluorescent ligand, TRANSFERASE; TRANSFERASE
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	27.85 Å
Radius of gyration Rg (electron density) rg_electron	27.34 Å
Forward intensity I(0) i0	99434200.00
Molecular weight molecular_weight	77718.0 kDa
Excluded volume excluded_volume	96907 Å³
Envelope volume envelope_volume	113810 Å³
Hydration-shell volume shell_volume	34851 Å³
Envelope diameter envelope_diameter	98.9 Å
Shell Rg shell_rg	34.57 Å
Envelope Rg envelope_rg	27.52 Å
Shape Rg shape_rg	27.36 Å
Total Rg total_rg	27.96 Å
Total atoms total_atoms	5439
Residues n_residues	711
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	94.7 Å
Rg (real space) rg_real	27.91 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	9.9430e+07
I(0) uncertainty (real space) i0_real_error	1.3670e+06
Rg (reciprocal space) rg_reciprocal	27.89 Å
I(0) (reciprocal space) i0_reciprocal	99430000.0000
Solution quality estimate total_estimate	0.8670
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.6 Å
Skewness Skewness skewness	0.459
Kurtosis Kurtosis kurtosis	-0.161
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	41430000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.789; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.925

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Purine nucleoside phosphorylase DeoD-type
Molecular weight formula_weight	25981.0 kDa
EC 编号 ec_number	2.4.2.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,B
Atom count atom_count	5614

MATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSNHIRTHEQTTAAERQTTFNDMIKIALESVLLGDKE

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	N,2,3-etheno-2-aminopurine
Molecular weight formula_weight	159.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	175

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8. Citations (1)

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Unit-cell length a length_a	120.525 Å
Unit-cell length b length_b	120.525 Å
Unit-cell length c length_c	241.206 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	36

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	hexagonal

Resolution resolution	2.120 Å
Low-resolution limit resolution_low	48.220 Å
R factor r_factor	0.2058
R_work r_work	0.2044
R_free r_free	0.2331

fit	/app/data/saxs_computation/fx/9fxe/9fxe.fit
pddf	/app/data/pr_computation/fx/9fxe/9fxe.pr.out
profile	/app/data/saxs_computation/fx/9fxe/9fxe.dat

D204N mutant of Purine Nucleoside Phosphorylase from E.coli in complex with N2,3-etheno-2-aminopurine

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

Purine nucleoside phosphorylase DeoD-type

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction