1d7a

CRYSTAL STRUCTURE OF E. COLI PURE-MONONUCLEOTIDE COMPLEX.

Method: X-RAY DIFFRACTION

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

PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	5-AMINOIMIDAZOLE RIBONUCLEOTIDE × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PUR6_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–161； UniProt 7–167 Author chain B； PDBConstruct 1–161； UniProt 7–167 Author chain C； PDBConstruct 1–161； UniProt 7–167 Author chain D； PDBConstruct 1–161； UniProt 7–167 Author chain L； PDBConstruct 1–161； UniProt 7–167 Author chain M； PDBConstruct 1–161； UniProt 7–167 Author chain N； PDBConstruct 1–161； UniProt 7–167 Author chain O； PDBConstruct 1–161； UniProt 7–167

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	1d7a
Deposition date deposition_date	1999-10-16
Structure title title	CRYSTAL STRUCTURE OF E. COLI PURE-MONONUCLEOTIDE COMPLEX.
Keywords keywords	THREE-LAYER (ALPHA-BETA-ALPHA) SANDWICH N5-CAIR MUTASE (PURE), AMINOIMIDAZOLE RIBONUCLEOTIDE (AIR), LYASE; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1d7a__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1d7a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1d7a__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.55 Å
Rg (electron density)	31.37 Å
Total Rg	31.80 Å
Atom count	9604
Residues	1256
Excluded volume	171310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1d7a__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE
Molecular weight formula_weight	17113.9 kDa
EC 编号 ec_number	4.1.1.21
Mutation mutation	M14(MSE), M23(MSE), M79(MSE), M110(MSE)
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,L,M,N,O
Atom count atom_count	9724

GARVAIVMGSKSDWATMQFAAEIFEILNVPHHVEVVSAHRTPDKLFSFAESAEENGYQVIIAGAGGAAHLPGMIAAKTLVPVLGVPVQSAALSGVDSLYSIVQMPRGIPVGTLAIGKAGAANAALLAAQILATHDKELHQRLNDWRKAQTDEVLENPDPRG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	5-AMINOIMIDAZOLE RIBONUCLEOTIDE
Molecular weight formula_weight	295.2 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	120

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1d7aa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.8 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
Family Family family	c.23.8.1 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)

Domain ID domain_id	d1d7ab_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.8 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
Family Family family	c.23.8.1 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)

Domain ID domain_id	d1d7ac_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.8 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
Family Family family	c.23.8.1 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)

Domain ID domain_id	d1d7ad_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.8 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
Family Family family	c.23.8.1 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)

Domain ID domain_id	d1d7al_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.8 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
Family Family family	c.23.8.1 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)

Domain ID domain_id	d1d7am_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.8 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
Family Family family	c.23.8.1 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)

Domain ID domain_id	d1d7an_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.8 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
Family Family family	c.23.8.1 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)

Domain ID domain_id	d1d7ao_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.8 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)
Family Family family	c.23.8.1 — N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE)

CATH v4.4 (8 domains)

Domain ID domain_id	1d7aA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

Domain ID domain_id	1d7aB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

Domain ID domain_id	1d7aC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

Domain ID domain_id	1d7aD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

Domain ID domain_id	1d7aL00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

Domain ID domain_id	1d7aM00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

Domain ID domain_id	1d7aN00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

Domain ID domain_id	1d7aO00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

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7. Citations (6)

Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway.

Structure Fold.Des. (1999)

PMID: 10574791 · DOI: 10.1016/S0969-2126(00)80029-5 PRIMARY

;Evidence for the Direct Transfer of the Carboxylate of N5-Carboxyaminoimidazole Ribonucleotide (N5-Cair) to Generate 4-Carboxy-5- Aminoimidazole Ribonucleotide Catalyzed by Escherichia Coli Pure, an N5-Cair Mutase ;

Biochemistry (1999)

DOI: 10.1021/bi9827159

;Reactions Catalyzed by 5-Aminoimidazole Ribonucleotide Carboxylases from Escherichia Coli and Gallus Gallus: A Case for Divergent Catalytic Mechanisms ;

Biochemistry (1994)

;N5-Carboxyaminoimidazole Ribonucleotide: Evidence for a New Intermediate and Two New Enzymatic Activities in the De Novo Purine Biosynthetic Pathway of Escherichia Coli ;

Biochemistry (1994)

;Nucleotide Sequence Analysis of the Purek Operon Encoding 5'-Phosphoribosyl-5-Aminoimidazole Carboxylase of Escherichia Coli K-12 ;

J.Bacteriol. (1989)

;Identification and Sequence Analysis of Escherichia Coli Pure and Purk Genes Encoding 5'-Phosphoribosyl-5-Amino-4-Imidazole Carboxylase for De Novo Purine Biosynthesis ;

J.Bacteriol. (1989)

Unit-cell length a length_a	86.920 Å
Unit-cell length b length_b	94.550 Å
Unit-cell length c length_c	149.960 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	32

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	25.000 Å
R factor r_factor	0.2000
R_work r_work	0.2030
R_free r_free	0.2390

CRYSTAL STRUCTURE OF E. COLI PURE-MONONUCLEOTIDE COMPLEX.

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

PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1d7a__assembly_1__model_1

1d7a__assembly_1__model_1 | I(q)

1d7a__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (6)

CRYSTAL STRUCTURE OF E. COLI PURE-MONONUCLEOTIDE COMPLEX.

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

PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1d7a__assembly_1__model_1

1d7a__assembly_1__model_1 | I(q)

1d7a__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (6)