SAXSdb — 9k03

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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 14–334 Chain B； UniProt 14–334	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

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 9K03	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 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 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 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
9K04 Crystal structure of Pyrococcus abyssi AIR synthetase H239A mutant bound to ADP and Pi Deposited 2024-10-15	Different ligand/ion 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 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 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 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
9VNW Crystal structure of Pyrococcus abyssi AIR synthetase with an N-terminal 54-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 56–334（279 aa）	Not recorded	No recorded non-water small molecule	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

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 1–321； UniProt 14–334 Author chain B； PDBConstruct 1–321； UniProt 14–334

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	9k03
Deposition date deposition_date	2024-10-15
Structure title title	Crystal structure of Pyrococcus abyssi AIR synthetase H239A mutant bound to AMPPNP
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	26.46 Å
Radius of gyration Rg (electron density) rg_electron	25.65 Å
Forward intensity I(0) i0	77841300.00
Molecular weight molecular_weight	71628.0 kDa
Excluded volume excluded_volume	90710 Å³
Envelope volume envelope_volume	103220 Å³
Hydration-shell volume shell_volume	33253 Å³
Envelope diameter envelope_diameter	86.8 Å
Shell Rg shell_rg	33.81 Å
Envelope Rg envelope_rg	25.84 Å
Shape Rg shape_rg	25.70 Å
Total Rg total_rg	26.31 Å
Total atoms total_atoms	5026
Residues n_residues	642
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	84.6 Å
Rg (real space) rg_real	26.45 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	7.7840e+07
I(0) uncertainty (real space) i0_real_error	1.0820e+06
Rg (reciprocal space) rg_reciprocal	26.45 Å
I(0) (reciprocal space) i0_reciprocal	77840000.0000
Solution quality estimate total_estimate	0.8855
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.6 Å
Skewness Skewness skewness	0.403
Kurtosis Kurtosis kurtosis	-0.223
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	34050000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.925

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Phosphoribosylformylglycinamidine cyclo-ligase
Molecular weight formula_weight	35223.7 kDa
EC 编号 ec_number	6.3.3.1
Mutation mutation	H239A
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	5343

TARALREIIRTARETFKLRKGKVGEPGDIGHYAALLDFGNFYLAMTTDGVGTKVLVAEAVGKFDTIGIDMIAMNVNDLLCVGAEPLALVDYFAVKEPNEEVFKQVAKGLYKGAEEAGVAIVGGETAVMPDLINGYDLAGTAIGIVEKGKVITGERIRPGDSVIGISSSGIHSNGLTLARKLLIPKYGLDYEYEGRKLWEWLLEPTRIYVRPILELINSVEVHGLAAITGGGLLNLKRLTNYGFELEMPPIEGIFKLIHENGVPLDEMFRVFNMGVGFIVVVPQEEKEEALEILSRHYKSYELGNVTRELGKIKVKNYGITL

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	301

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8. Citations (1)

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Unit-cell length a length_a	103.375 Å
Unit-cell length b length_b	113.038 Å
Unit-cell length c length_c	70.550 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	28.260 Å
R factor r_factor	0.1658
R_work r_work	0.1637
R_free r_free	0.2054

fit	/app/data/saxs_computation/k0/9k03/9k03.fit
pddf	/app/data/pr_computation/k0/9k03/9k03.pr.out
profile	/app/data/saxs_computation/k0/9k03/9k03.dat

Crystal structure of Pyrococcus abyssi AIR synthetase H239A mutant bound to AMPPNP

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