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6xeq

Crystal structure of the tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter oxidans

Method: X-RAY DIFFRACTION Dmax: 115.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

6-phosphogluconate dehydrogenase

Gluconobacter oxydans

UniProt G5EBD7

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–332 Chain B； UniProt 1–332 Chain C； UniProt 1–332 Chain D； UniProt 1–332 Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；292 K；2 M (NH4)2SO4 and 5% (v/v) 2-propanol Resolution 3.20 Å R-free 0.286

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 6XEQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10GW Crystal structure of tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter oxydans in complex with 6-phosphogluconate Deposited 2026-01-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–332（332 aa）
Chain B 1–332（332 aa）
Chain C 1–332（332 aa）
Chain D 1–332（332 aa）
Not recorded 6PG 6-PHOSPHOGLUCONIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291.15 K；0.1 M BIS-TRIS at pH 6.5 and 28% w/v polyethylene glycol monomethyl ether 2,000.
Resolution 2.00 Å R-free 0.224

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

View Construct and Data Evidence
UniProt name 6PGDH_GLUOX
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 22–353； UniProt 1–332 Author chain B； PDBConstruct 22–353； UniProt 1–332 Author chain C； PDBConstruct 22–353； UniProt 1–332 Author chain D； PDBConstruct 22–353； UniProt 1–332

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 6xeq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6xeq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6xeq
Deposition date deposition_date2020-06-13
Structure title titleCrystal structure of the tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter oxidans
Keywords keywordsDehydrogenase, pentose phosphate pathway, tetramer, OXIDOREDUCTASE; OXIDOREDUCTASE
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_guinier36.04 Å
Radius of gyration Rg (electron density) rg_electron35.29 Å
Forward intensity I(0) i0316026000.00
Molecular weight molecular_weight137650.0 kDa
Excluded volume excluded_volume169720 ų
Envelope volume envelope_volume217070 ų
Hydration-shell volume shell_volume50845 ų
Envelope diameter envelope_diameter118.5 Å
Shell Rg shell_rg41.90 Å
Envelope Rg envelope_rg35.42 Å
Shape Rg shape_rg35.29 Å
Total Rg total_rg35.70 Å
Total atoms total_atoms9654
Residues n_residues1271
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 dmax115.2 Å
Rg (real space) rg_real35.96 Å
Rg uncertainty (real space) rg_real_error0.96 Å
I(0) (real space) i0_real3.1600e+08
I(0) uncertainty (real space) i0_real_error5.6290e+06
Rg (reciprocal space) rg_reciprocal36.02 Å
I(0) (reciprocal space) i0_reciprocal316000000.0000
Solution quality estimate total_estimate0.8975
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.5 Å
Skewness Skewness skewness0.214
Kurtosis Kurtosis kurtosis-0.568
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha143000000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.866
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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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8. Citations (1)

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9. Files and Curves (10)