1kxj

The Crystal Structure of Glutamine Amidotransferase from Thermotoga maritima

Method: X-RAY DIFFRACTION Dmax: 79.2 Å Quality: GOOD

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

Amidotransferase hisH

Thermotoga maritima

UniProt Q9X0C8

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–201 Not recorded PO4 PHOSPHATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;298 K;2 M mono-Ammonium dihydrogen Phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K Resolution 2.80 Å R-free 0.274
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–201 Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;298 K;2 M mono-Ammonium dihydrogen Phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K Resolution 2.80 Å R-free 0.274

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.

8 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HIS5_THEMA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–203; UniProt 1–201 Author chain B; PDBConstruct 3–203; UniProt 1–201

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 1kxj

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1kxj
Deposition date deposition_date2002-01-31
Structure title titleThe Crystal Structure of Glutamine Amidotransferase from Thermotoga maritima
Keywords keywordsalpha-beta-alpha, Structural genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.54
Radius of gyration Rg (electron density) rg_electron23.68
Forward intensity I(0) i037855100.00
Molecular weight molecular_weight46712.0 kDa
Excluded volume excluded_volume58127 ų
Envelope volume envelope_volume69283 ų
Hydration-shell volume shell_volume24776 ų
Envelope diameter envelope_diameter79.6
Shell Rg shell_rg30.54
Envelope Rg envelope_rg23.88
Shape Rg shape_rg23.69
Total Rg total_rg24.44
Total atoms total_atoms3282
Residues n_residues403
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax79.2
Rg (real space) rg_real24.59
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real3.7860e+07
I(0) uncertainty (real space) i0_real_error5.2010e+05
Rg (reciprocal space) rg_reciprocal24.58
I(0) (reciprocal space) i0_reciprocal37850000.0000
Solution quality estimate total_estimate0.8830
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.4
Skewness Skewness skewness0.408
Kurtosis Kurtosis kurtosis-0.383
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9781000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.939

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1kxja1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)
Domain ID domain_idd1kxja2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1kxjb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.16 — Class I glutamine amidotransferase-like
Family Family familyc.23.16.1 — Class I glutamine amidotransferases (GAT)
Domain ID domain_idd1kxjb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id1kxjA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain
Domain ID domain_id1kxjB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily880 — Class I glutamine amidotransferase (GATase) domain

8. Citations (1)

9. Files and Curves (10)