SAXSdb — 9vnw

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

Phosphoribosylformylglycinamidine cyclo-ligase

Pyrococcus abyssi GE5

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 56–334	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；Jeffamine T-403, Jeffamine ED-2003, Tris	Resolution 2.50 Å R-free 0.234

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 9VNW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9K00 Crystal structure of Pyrococcus abyssi AIR synthetase Deposited 2024-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–334（321 aa） Chain B 14–334（321 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；lithium sulfate, poly(acrylic acid sodium salt) 2100, HEPES	Resolution 2.00 Å R-free 0.213
9K01 Crystal structure of Pyrococcus abyssi AIR synthetase bound to ADP Deposited 2024-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–334（321 aa） Chain B 14–334（321 aa）	Not recorded	SO4 SULFATE ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；lithium sulfate, poly(acrylic acid sodium salt) 2100, HEPES	Resolution 1.60 Å R-free 0.193
9K02 Crystal structure of Pyrococcus abyssi AIR synthetase bound to ADP and Mg(II) Deposited 2024-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–334（321 aa） Chain B 14–334（321 aa）	Not recorded	SO4 SULFATE ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；lithium sulfate, poly(acrylic acid sodium salt) 2100, HEPES	Resolution 2.00 Å R-free 0.207
9K03 Crystal structure of Pyrococcus abyssi AIR synthetase H239A mutant bound to AMPPNP Deposited 2024-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–334（321 aa） Chain B 14–334（321 aa）	Mutation：H239A Mutation：H239A	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MN MANGANESE (II) ION × 4 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；potassium chloride, pentaerythritol ethoxylate, glycine	Resolution 2.25 Å R-free 0.205
9K04 Crystal structure of Pyrococcus abyssi AIR synthetase H239A mutant bound to ADP and Pi Deposited 2024-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–334（321 aa） Chain B 14–334（321 aa）	Mutation：H239A Mutation：H239A	ADP ADENOSINE-5'-DIPHOSPHATE × 2 PO4 PHOSPHATE ION × 2 MN MANGANESE (II) ION × 4 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；potassium chloride, pentaerythritol ethoxylate, glycine	Resolution 1.60 Å R-free 0.177
9K05 Crystal structure of Pyrococcus abyssi AIR synthetase N186A mutant bound to FGAR and AMP Deposited 2024-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–334（334 aa） Chain B 1–334（334 aa）	Mutation：N186A Mutation：N186A	FGR N-(N-FORMYLGLYCYL)-5-O-PHOSPHONO-BETA-D-RIBOFURANOSYLAMINE × 2 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；lithium sulfate, poly(acrylic acid sodium salt) 2100, HEPES	Resolution 1.80 Å R-free 0.193
9K06 Crystal structure of Pyrococcus abyssi AIR synthetase with residues 51-54 replaced by Neisseria gonorrhoeae residues 49-56 Deposited 2024-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–334（321 aa） Chain B 14–334（321 aa）	Not recorded	SO4 SULFATE ION × 2 FLC CITRATE ANION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；lithium sulfate, 2-propanol, sodium citrate	Resolution 1.70 Å R-free 0.196
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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 163–334（172 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
9VNV Crystal structure of Pyrococcus abyssi AIR synthetase with an N-terminal 43-residues deletion Deposited 2025-07-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 44–334（291 aa） Chain B 44–334（291 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；303 K；sodium thiocyanate, pentaerythritol propoxylate (5/4 PO/OH), HEPES	Resolution 2.50 Å R-free 0.241

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PUR5_PYRAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–281； UniProt 56–334

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	9vnw
Deposition date deposition_date	2025-07-01
最后修订 last_revision	2026-02-11
Structure title title	Crystal structure of Pyrococcus abyssi AIR synthetase with an N-terminal 54-residues deletion
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	20.07 Å
Radius of gyration Rg (electron density) rg_electron	19.16 Å
Forward intensity I(0) i0	14776500.00
Molecular weight molecular_weight	30616.0 kDa
Excluded volume excluded_volume	39027 Å³
Envelope volume envelope_volume	44507 Å³
Hydration-shell volume shell_volume	19404 Å³
Envelope diameter envelope_diameter	67.3 Å
Shell Rg shell_rg	25.36 Å
Envelope Rg envelope_rg	19.39 Å
Shape Rg shape_rg	19.16 Å
Total Rg total_rg	20.04 Å
Total atoms total_atoms	2157
Residues n_residues	281
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	66.3 Å
Rg (real space) rg_real	20.01 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	1.4780e+07
I(0) uncertainty (real space) i0_real_error	1.8060e+05
Rg (reciprocal space) rg_reciprocal	20.02 Å
I(0) (reciprocal space) i0_reciprocal	14780000.0000
Solution quality estimate total_estimate	0.8882
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.7 Å
Skewness Skewness skewness	0.251
Kurtosis Kurtosis kurtosis	-0.421
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4791000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	88.693 Å
Unit-cell length b length_b	88.693 Å
Unit-cell length c length_c	182.600 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	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	orthorhombic

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	29.660 Å
R factor r_factor	0.1971
R_work r_work	0.1951
R_free r_free	0.2339

Description description	Phosphoribosylformylglycinamidine cyclo-ligase
Molecular weight formula_weight	30675.5 kDa
EC 编号 ec_number	6.3.3.1
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2175

Crystal structure of Pyrococcus abyssi AIR synthetase with an N-terminal 54-residues deletion

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Pyrococcus abyssi GE5
NCBI Class编号 ncbi_taxonomy_id	272844
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	18

fit	/app/data/saxs_computation/vn/9vnw/9vnw.fit
pddf	/app/data/pr_computation/vn/9vnw/9vnw.pr.out
profile	/app/data/saxs_computation/vn/9vnw/9vnw.dat