1cli

X-RAY CRYSTAL STRUCTURE OF AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE (PURM), FROM THE E. COLI PURINE BIOSYNTHETIC PATHWAY, AT 2.5 A RESOLUTION

Method: X-RAY DIFFRACTION D_max: 127.2 Å Quality: GOOD

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

PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)

Escherichia coli

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 B； UniProt 2–345 Chain D； UniProt 2–345	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–345 Chain D； UniProt 2–345	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
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–345 Chain B； UniProt 2–345	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
4	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–345 Chain B； UniProt 2–345 Chain C； UniProt 2–345 Chain D； UniProt 2–345	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

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 1CLI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9JZW Crystal structure of E. coli AIR synthetase Deposited 2024-10-15	Different construct Different experimental conditions 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 × 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
9JZW Crystal structure of E. coli AIR synthetase Deposited 2024-10-15	Different construct Different ligand/ion Different experimental conditions 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	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
9JZX Crystal structure of E. coli AIR synthetase bound to AMP Deposited 2024-10-15	Different construct Different ligand/ion Different experimental conditions 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 construct Different ligand/ion Different experimental conditions 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 5 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 2–345； UniProt 2–345 Author chain B； PDBConstruct 2–345； UniProt 2–345 Author chain C； PDBConstruct 2–345； UniProt 2–345 Author chain D； PDBConstruct 2–345； UniProt 2–345

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.

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	1cli
Deposition date deposition_date	1999-04-28
Structure title title	X-RAY CRYSTAL STRUCTURE OF AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE (PURM), FROM THE E. COLI PURINE BIOSYNTHETIC PATHWAY, AT 2.5 A RESOLUTION
Keywords keywords	AIR SYNTHETASE, PURM, PURINE BIOSYNTHESIS, TRIFUNCTIONAL ENZYME, PURL, FGAR AMIDOTRANSFERASE, NOVEL FOLD, 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	37.95 Å
Radius of gyration Rg (electron density) rg_electron	37.57 Å
Forward intensity I(0) i0	310675000.00
Molecular weight molecular_weight	142610.0 kDa
Excluded volume excluded_volume	178410 Å³
Envelope volume envelope_volume	226670 Å³
Hydration-shell volume shell_volume	51257 Å³
Envelope diameter envelope_diameter	132.9 Å
Shell Rg shell_rg	42.48 Å
Envelope Rg envelope_rg	37.39 Å
Shape Rg shape_rg	37.61 Å
Total Rg total_rg	37.76 Å
Total atoms total_atoms	10010
Residues n_residues	1332
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	127.2 Å
Rg (real space) rg_real	38.11 Å
Rg uncertainty (real space) rg_real_error	1.35 Å
I(0) (real space) i0_real	3.1070e+08
I(0) uncertainty (real space) i0_real_error	5.7280e+06
Rg (reciprocal space) rg_reciprocal	38.01 Å
I(0) (reciprocal space) i0_reciprocal	310600000.0000
Solution quality estimate total_estimate	0.8693
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.4 Å
Skewness Skewness skewness	0.440
Kurtosis Kurtosis kurtosis	-0.291
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	83950000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.761

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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	PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)
Molecular weight formula_weight	36858.9 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	10513

VTDKTSLSYKDAGVDIDAGNALVGRIKGVVKKTRRPEVMGGLGGFGALCALPQKYREPVLVSGTDGVGTKLRLAMDLKRHDTIGIDLVAMCVNDLVVQGAEPLFFLDYYATGKLDVDTASAVISGIAEGCLQSGCSLVGGETAEMPGMYHGEDYDVAGFCVGVVEKSEIIDGSKVSDGDVLIALGSSGPHSNGYSLVRKILEVSGCDPQTTELDGKPLADHLLAPTRIYVKSVLELIEKVDVHAIAHLTGGGFWENIPRVLPDNTQAVIDESSWQWPEVFNWLQTAGNVEHHEMYRTFNCGVGMIIALPAPEVDKALALLNANGENAWKIGIIKASDSEQRVVIE

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21

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	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	503

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1clia1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
Family Family family	d.79.4.1 — PurM N-terminal domain-like

Domain ID domain_id	d1clia2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.139 — PurM C-terminal domain-like
Superfamily Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
Family Family family	d.139.1.1 — PurM C-terminal domain-like

Domain ID domain_id	d1clib1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
Family Family family	d.79.4.1 — PurM N-terminal domain-like

Domain ID domain_id	d1clib2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.139 — PurM C-terminal domain-like
Superfamily Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
Family Family family	d.139.1.1 — PurM C-terminal domain-like

Domain ID domain_id	d1clic1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
Family Family family	d.79.4.1 — PurM N-terminal domain-like

Domain ID domain_id	d1clic2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.139 — PurM C-terminal domain-like
Superfamily Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
Family Family family	d.139.1.1 — PurM C-terminal domain-like

Domain ID domain_id	d1clid1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.4 — PurM N-terminal domain-like
Family Family family	d.79.4.1 — PurM N-terminal domain-like

Domain ID domain_id	d1clid2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.139 — PurM C-terminal domain-like
Superfamily Superfamily superfamily	d.139.1 — PurM C-terminal domain-like
Family Family family	d.139.1.1 — PurM C-terminal domain-like

CATH v4.4 (8 domains)

Domain ID domain_id	1cliA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	10 — PurM-like, N-terminal domain

Domain ID domain_id	1cliA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — PurM-like C-terminal domain

Domain ID domain_id	1cliB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	10 — PurM-like, N-terminal domain

Domain ID domain_id	1cliB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — PurM-like C-terminal domain

Domain ID domain_id	1cliC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	10 — PurM-like, N-terminal domain

Domain ID domain_id	1cliC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — PurM-like C-terminal domain

Domain ID domain_id	1cliD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	10 — PurM-like, N-terminal domain

Domain ID domain_id	1cliD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	650 — Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — PurM-like C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	71.170 Å
Unit-cell length b length_b	211.680 Å
Unit-cell length c length_c	94.450 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	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1920
R_free r_free	0.2640

fit	/app/data/saxs_computation/cl/1cli/1cli.fit
pddf	/app/data/pr_computation/cl/1cli/1cli.pr.out
profile	/app/data/saxs_computation/cl/1cli/1cli.dat