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1hw6

CRYSTAL STRUCTURE OF APO-2,5-DIKETO-D-GLUCONATE REDUCTASE

Method: X-RAY DIFFRACTION Dmax: 57.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

2,5-DIKETO-D-GLUCONIC ACID REDUCTASE

Corynebacterium sp.

UniProt P06632

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 1–278 Not recorded MG MAGNESIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 4000, 0.2M MgCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.90 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 1HW6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A80 Native 2,5-DIKETO-D-GLUCONIC acid reductase a from CORYNBACTERIUM SP. complexed with nadph Deposited 1998-03-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–278（277 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.1；pH 7.1
Resolution 2.10 Å
1M9H Corynebacterium 2,5-DKGR A and Phe 22 replaced with Tyr (F22Y), Lys 232 replaced with Gly (K232G), Arg 238 replaced with His (R238H)and Ala 272 replaced with Gly (A272G)in presence of NADH cofactor Deposited 2002-07-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 0–277（278 aa）
Mutation：F22Y, K232G, R238H, A272G SO4 SULFATE ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；lithium sulfate monohydrate, hepes-sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.261
1M9H Corynebacterium 2,5-DKGR A and Phe 22 replaced with Tyr (F22Y), Lys 232 replaced with Gly (K232G), Arg 238 replaced with His (R238H)and Ala 272 replaced with Gly (A272G)in presence of NADH cofactor Deposited 2002-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 0–277（278 aa）
Mutation：F22Y, K232G, R238H, A272G SO4 SULFATE ION × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；lithium sulfate monohydrate, hepes-sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.261

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

View Construct and Data Evidence
UniProt name DKGA_CORSC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–278； UniProt 1–278

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 1hw6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1hw6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1hw6
Deposition date deposition_date2001-01-09
Structure title titleCRYSTAL STRUCTURE OF APO-2,5-DIKETO-D-GLUCONATE REDUCTASE
Keywords keywordsaldo-keto reductase, TIM barrel, 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_guinier19.07 Å
Radius of gyration Rg (electron density) rg_electron17.78 Å
Forward intensity I(0) i013033700.00
Molecular weight molecular_weight27376.0 kDa
Excluded volume excluded_volume34363 ų
Envelope volume envelope_volume38887 ų
Hydration-shell volume shell_volume18290 ų
Envelope diameter envelope_diameter57.8 Å
Shell Rg shell_rg23.88 Å
Envelope Rg envelope_rg17.87 Å
Shape Rg shape_rg17.77 Å
Total Rg total_rg18.75 Å
Total atoms total_atoms1935
Residues n_residues257
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 dmax57.2 Å
Rg (real space) rg_real18.95 Å
Rg uncertainty (real space) rg_real_error0.26 Å
I(0) (real space) i0_real1.3030e+07
I(0) uncertainty (real space) i0_real_error1.5780e+05
Rg (reciprocal space) rg_reciprocal18.96 Å
I(0) (reciprocal space) i0_reciprocal13030000.0000
Solution quality estimate total_estimate0.9107
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.6 Å
Skewness Skewness skewness0.123
Kurtosis Kurtosis kurtosis-0.559
Angular range angular_range— – 0.4150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4527000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1hw6a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.7 — NAD(P)-linked oxidoreductase
Family Family familyc.1.7.1 — Aldo-keto reductases (NADP)

CATH v4.4 (1 domains)

Domain ID domain_id1hw6A00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily100 — NADP-dependent oxidoreductase domain
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8. Citations (1)

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9. Files and Curves (10)