1d7a

CRYSTAL STRUCTURE OF E. COLI PURE-MONONUCLEOTIDE COMPLEX.

Method: X-RAY DIFFRACTION D_max: 114.1 Å Quality: GOOD

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

PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 7–167 Chain B； UniProt 7–167 Chain C； UniProt 7–167 Chain D； UniProt 7–167 Chain L； UniProt 7–167 Chain M； UniProt 7–167 Chain N； UniProt 7–167 Chain O； UniProt 7–167	Fragment：CATALYTIC SUBUNIT Mutation：M14(MSE), M23(MSE), M79(MSE), M110(MSE) Non-standard monomer：Yes (specific site not provided by mmCIF)	AIR 5-AMINOIMIDAZOLE RIBONUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；281 K；PEG4000, Ammonium Acetate, TRIS.HCl, 4-CARBOXY AMINOIMIDAZOLE RIBONUCLEOTIDE (CAIR), pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 2.50 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 1D7A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QCZ CRYSTAL STRUCTURE OF E. COLI PURE, AN UNUSUAL MUTASE THAT CATALYZES THE CONVERSION OF N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE (N5-CAIR) TO 4-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE (CAIR) IN THE PURINE BIOSYNTHETIC PATHWAY Deposited 1999-05-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–169（169 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG400, TRIS.HCL, MAGNESIUM CHLORIDE, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 18K	Resolution 1.50 Å R-free 0.213

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

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.

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	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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.55 Å
Radius of gyration Rg (electron density) rg_electron	31.37 Å
Forward intensity I(0) i0	305817000.00
Molecular weight molecular_weight	137950.0 kDa
Excluded volume excluded_volume	171310 Å³
Envelope volume envelope_volume	203380 Å³
Hydration-shell volume shell_volume	50734 Å³
Envelope diameter envelope_diameter	97.6 Å
Shell Rg shell_rg	40.91 Å
Envelope Rg envelope_rg	31.39 Å
Shape Rg shape_rg	31.45 Å
Total Rg total_rg	31.80 Å
Total atoms total_atoms	9604
Residues n_residues	1256
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	114.1 Å
Rg (real space) rg_real	32.32 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	3.0580e+08
I(0) uncertainty (real space) i0_real_error	4.9280e+06
Rg (reciprocal space) rg_reciprocal	32.42 Å
I(0) (reciprocal space) i0_reciprocal	305800000.0000
Solution quality estimate total_estimate	0.7889
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	39.6 Å
Skewness Skewness skewness	0.094
Kurtosis Kurtosis kurtosis	-0.669
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	363900000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.751; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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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	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

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

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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7. 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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8. 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 ;