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1b6r

N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE FROM E. COLI

Method: X-RAY DIFFRACTION Dmax: 70.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)

OrganismNot specified

UniProt P09029

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 1–355 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.8；100MM HEPPS, PH 7.8 0.575 M AMMONIUM SULFATE Resolution 2.10 Å

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 1B6R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B6S STRUCTURE OF N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE Deposited 1999-01-18 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 1–355（355 aa）
Chain B 1–355（355 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.50 Å
1B6S STRUCTURE OF N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE Deposited 1999-01-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–355（355 aa）
Chain D 1–355（355 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.50 Å
3ETH Crystal structure of E. coli Purk in complex with MgATP Deposited 2008-10-08 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 1–355（355 aa）
Chain B 1–355（355 aa）
Mutation：E61Q, Q205R Mutation：E61Q, Q205R ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20-25% monomethylether poly(ethylene glycol) 5000, 10 mM MgATP, 10 mM aminopyrazole ribonucleotide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.228
3ETJ Crystal structure E. coli Purk in complex with Mg, ADP, and Pi Deposited 2008-10-08 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 1–355（355 aa）
Chain B 1–355（355 aa）
Mutation：E61Q, Q205R Mutation：E61Q, Q205R ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 PI HYDROGENPHOSPHATE ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；monomethylether poly(ethylene glycol) 5000, MgATP, 5-aminoimidazole ribonucleotide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.215

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PURK_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–355； UniProt 1–355

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

SAXS profile for 1b6r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b6r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b6r
Deposition date deposition_date1999-01-17
Structure title titleN5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE FROM E. COLI
Keywords keywordsATP-GRASP, CARBOXYPHOSPHATE, PURINE BIOSYNTHESIS, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.92 Å
Radius of gyration Rg (electron density) rg_electron20.90 Å
Forward intensity I(0) i025813100.00
Molecular weight molecular_weight38895.0 kDa
Excluded volume excluded_volume48753 ų
Envelope volume envelope_volume57453 ų
Hydration-shell volume shell_volume22886 ų
Envelope diameter envelope_diameter68.2 Å
Shell Rg shell_rg27.69 Å
Envelope Rg envelope_rg21.00 Å
Shape Rg shape_rg20.91 Å
Total Rg total_rg21.75 Å
Total atoms total_atoms2742
Residues n_residues349
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax70.6 Å
Rg (real space) rg_real21.79 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real2.5810e+07
I(0) uncertainty (real space) i0_real_error3.1350e+05
Rg (reciprocal space) rg_reciprocal21.82 Å
I(0) (reciprocal space) i0_reciprocal25810000.0000
Solution quality estimate total_estimate0.6220
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary28.4 Å
Skewness Skewness skewness0.153
Kurtosis Kurtosis kurtosis-0.541
Angular range angular_range— – 0.3600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9897000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.886; Stabil: 0.996; Sysdev: 0.145; Positv: 1.000; Valcen: 1.000; 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)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1b6ra1
Class classb — All beta proteins
Fold Fold foldb.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamilyb.84.2 — Rudiment single hybrid motif
Family Family familyb.84.2.1 — BC C-terminal domain-like
Domain ID domain_idd1b6ra2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.30 — PreATP-grasp domain
Superfamily Superfamily superfamilyc.30.1 — PreATP-grasp domain
Family Family familyc.30.1.1 — BC N-terminal domain-like
Domain ID domain_idd1b6ra3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.142 — ATP-grasp
Superfamily Superfamily superfamilyd.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family familyd.142.1.2 — BC ATP-binding domain-like

CATH v4.4 (3 domains)

Domain ID domain_id1b6rA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1b6rA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, B domain
Domain ID domain_id1b6rA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, A domain
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8. Citations (1)

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9. Files and Curves (10)