SAXSdb — 9jzw

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

Phosphoribosylformylglycinamidine cyclo-ligase

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–345 Chain B； UniProt 1–345	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；ammonium sulfate, 2-propanol	Resolution 2.10 Å R-free 0.239
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–345 Chain D； UniProt 1–345	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；ammonium sulfate, 2-propanol	Resolution 2.10 Å R-free 0.239

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 9JZW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CLI X-RAY CRYSTAL STRUCTURE OF AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE (PURM), FROM THE E. COLI PURINE BIOSYNTHETIC PATHWAY, AT 2.5 A RESOLUTION Deposited 1999-04-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2–345（344 aa） Chain D 2–345（344 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.50 Å R-free 0.264
1CLI X-RAY CRYSTAL STRUCTURE OF AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE (PURM), FROM THE E. COLI PURINE BIOSYNTHETIC PATHWAY, AT 2.5 A RESOLUTION Deposited 1999-04-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–345（344 aa） Chain D 2–345（344 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.50 Å R-free 0.264
1CLI X-RAY CRYSTAL STRUCTURE OF AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE (PURM), FROM THE E. COLI PURINE BIOSYNTHETIC PATHWAY, AT 2.5 A RESOLUTION Deposited 1999-04-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–345（344 aa） Chain B 2–345（344 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.50 Å R-free 0.264
1CLI X-RAY CRYSTAL STRUCTURE OF AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE (PURM), FROM THE E. COLI PURINE BIOSYNTHETIC PATHWAY, AT 2.5 A RESOLUTION Deposited 1999-04-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–345（344 aa） Chain B 2–345（344 aa） Chain C 2–345（344 aa） Chain D 2–345（344 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.50 Å R-free 0.264
9JZX Crystal structure of E. coli AIR synthetase bound to AMP Deposited 2024-10-15	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–345（345 aa） Chain B 1–345（345 aa）	Not recorded	SO4 SULFATE ION × 5 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；ammonium sulfate, 2-propanol	Resolution 2.50 Å R-free 0.245
9JZX Crystal structure of E. coli AIR synthetase bound to AMP Deposited 2024-10-15	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–345（345 aa） Chain D 1–345（345 aa）	Not recorded	SO4 SULFATE ION × 5 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；ammonium sulfate, 2-propanol	Resolution 2.50 Å R-free 0.245
9VNU Crystal structure of chimeric AIR synthetase constructed from E. coli (residues 1-168) and Pyrococcus abyssi (residues 163-334) Deposited 2025-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–168（168 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；pentaerythritol ethoxylate (3/4 EO/OH), magnesium chloride	Resolution 2.40 Å R-free 0.223

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PUR5_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–345； UniProt 1–345 Author chain B； PDBConstruct 1–345； UniProt 1–345 Author chain C； PDBConstruct 1–345； UniProt 1–345 Author chain D； PDBConstruct 1–345； UniProt 1–345

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	9jzw
Deposition date deposition_date	2024-10-15
Structure title title	Crystal structure of E. coli AIR synthetase
Keywords keywords	Purine synthesis, ATP hydrolysis, LIGASE; LIGASE
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	38.11 Å
Radius of gyration Rg (electron density) rg_electron	37.68 Å
Forward intensity I(0) i0	310841000.00
Molecular weight molecular_weight	141880.0 kDa
Excluded volume excluded_volume	177130 Å³
Envelope volume envelope_volume	227440 Å³
Hydration-shell volume shell_volume	51293 Å³
Envelope diameter envelope_diameter	132.0 Å
Shell Rg shell_rg	42.63 Å
Envelope Rg envelope_rg	37.47 Å
Shape Rg shape_rg	37.72 Å
Total Rg total_rg	37.85 Å
Total atoms total_atoms	9948
Residues n_residues	1318
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	128.2 Å
Rg (real space) rg_real	38.25 Å
Rg uncertainty (real space) rg_real_error	1.42 Å
I(0) (real space) i0_real	3.1080e+08
I(0) uncertainty (real space) i0_real_error	5.8350e+06
Rg (reciprocal space) rg_reciprocal	38.16 Å
I(0) (reciprocal space) i0_reciprocal	310800000.0000
Solution quality estimate total_estimate	0.8692
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.6 Å
Skewness Skewness skewness	0.428
Kurtosis Kurtosis kurtosis	-0.303
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	75180000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.753

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Phosphoribosylformylglycinamidine cyclo-ligase
Molecular weight formula_weight	36890.9 kDa
EC 编号 ec_number	6.3.3.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10548

MTDKTSLSYKDAGVDIDAGNALVGRIKGVVKKTRRPEVMGGLGGFGALCALPQKYREPVLVSGTDGVGTKLRLAMDLKRHDTIGIDLVAMCVNDLVVQGAEPLFFLDYYATGKLDVDTASAVISGIAEGCLQSGCSLVGGETAEMPGMYHGEDYDVAGFCVGVVEKSEIIDGSKVSDGDVLIALGSSGPHSNGYSLVRKILEVSGCDPQTTELDGKPLADHLLAPTRIYVKSVLELIEKVDVHAIAHLTGGGFWENIPRVLPDNTQAVIDESSWQWPEVFNWLQTAGNVEHHEMYRTFNCGVGMIIALPAPEVDKALALLNANGENAWKIGIIKASDSEQRVVIE

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	567

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8. Citations (1)

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Unit-cell length a length_a	71.697 Å
Unit-cell length b length_b	94.408 Å
Unit-cell length c length_c	211.056 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	25.360 Å
R factor r_factor	0.2002
R_work r_work	0.1981
R_free r_free	0.2391

fit	/app/data/saxs_computation/jz/9jzw/9jzw.fit
pddf	/app/data/pr_computation/jz/9jzw/9jzw.pr.out
profile	/app/data/saxs_computation/jz/9jzw/9jzw.dat

Crystal structure of E. coli AIR synthetase

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

Phosphoribosylformylglycinamidine cyclo-ligase

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