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1xru

Crystal Structure of 5-keto-4-deoxyuronate Isomerase from Eschericia coli

Method: X-RAY DIFFRACTION Dmax: 81.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

Escherichia coli

UniProt Q46938

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–278 Chain B； UniProt 1–278 Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 1PE PENTAETHYLENE GLYCOL × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；277 K；PEG 400, calcium chloride, HEPES, pH 7, VAPOR DIFFUSION, temperature 277K Resolution 1.94 Å R-free 0.191
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–278 Chain B； UniProt 1–278 Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；277 K；PEG 400, calcium chloride, HEPES, pH 7, VAPOR DIFFUSION, temperature 277K Resolution 1.94 Å R-free 0.191

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 1XRU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1X8M X-ray structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from Escherichia coli Deposited 2004-08-18 Different construct Different mutation/modification Different oligomeric state 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 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Sodium Citrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.280
1X8M X-ray structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from Escherichia coli Deposited 2004-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–278（277 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Sodium Citrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.280
1X8M X-ray structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from Escherichia coli Deposited 2004-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 2–278（277 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Sodium Citrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.280
1X8M X-ray structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from Escherichia coli Deposited 2004-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 2–278（277 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Sodium Citrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.280
1X8M X-ray structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from Escherichia coli Deposited 2004-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 2–278（277 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Sodium Citrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.280
1X8M X-ray structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from Escherichia coli Deposited 2004-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 2–278（277 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Sodium Citrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.280

1 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KDUI_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–281； UniProt 1–278 Author chain B； PDBConstruct 4–281； 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 1xru

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1xru
Deposition date deposition_date2004-10-15
Structure title titleCrystal Structure of 5-keto-4-deoxyuronate Isomerase from Eschericia coli
Keywords keywordsBETA BARREL, CUPIN, ISOMERASE; ISOMERASE
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_guinier25.10 Å
Radius of gyration Rg (electron density) rg_electron24.36 Å
Forward intensity I(0) i071984200.00
Molecular weight molecular_weight63996.0 kDa
Excluded volume excluded_volume78576 ų
Envelope volume envelope_volume90207 ų
Hydration-shell volume shell_volume30467 ų
Envelope diameter envelope_diameter85.1 Å
Shell Rg shell_rg32.23 Å
Envelope Rg envelope_rg24.59 Å
Shape Rg shape_rg24.38 Å
Total Rg total_rg25.09 Å
Total atoms total_atoms4408
Residues n_residues540
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 dmax81.0 Å
Rg (real space) rg_real25.07 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real7.1980e+07
I(0) uncertainty (real space) i0_real_error1.0590e+06
Rg (reciprocal space) rg_reciprocal25.08 Å
I(0) (reciprocal space) i0_reciprocal71980000.0000
Solution quality estimate total_estimate0.8900
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.6 Å
Skewness Skewness skewness0.345
Kurtosis Kurtosis kurtosis-0.335
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16410000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.866; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.978
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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1xrua1
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.1 — RmlC-like cupins
Family Family familyb.82.1.13 — KduI-like
Domain ID domain_idd1xrua2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1xrub2
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.1 — RmlC-like cupins
Family Family familyb.82.1.13 — KduI-like
Domain ID domain_idd1xrub3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id1xruA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily520 — pectin degrading enzyme 5-keto 4- deoxyuronate isomerase, domain 1
Domain ID domain_id1xruA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
Domain ID domain_id1xruB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily520 — pectin degrading enzyme 5-keto 4- deoxyuronate isomerase, domain 1
Domain ID domain_id1xruB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
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8. Citations (1)

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9. Files and Curves (10)