1x8m

X-ray structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from Escherichia coli

Method: X-RAY DIFFRACTION D_max: 151.2 Å Quality: GOOD

▼

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

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

Escherichia coli

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 2–278	Not recorded	No other associated polymer	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 2–278	Not recorded	No other associated polymer	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 2–278	Not recorded	No other associated polymer	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 2–278	Not recorded	No other associated polymer	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
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 2–278	Not recorded	No other associated polymer	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
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 2–278	Not recorded	No other associated polymer	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

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 1X8M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XRU Crystal Structure of 5-keto-4-deoxyuronate Isomerase from Eschericia coli Deposited 2004-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–278（278 aa） Chain B 1–278（278 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) 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
1XRU Crystal Structure of 5-keto-4-deoxyuronate Isomerase from Eschericia coli Deposited 2004-10-15	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 1–278（278 aa） Chain B 1–278（278 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) 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

1 other PDB entries and 2 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 4–280； UniProt 2–278 Author chain B； PDBConstruct 4–280； UniProt 2–278 Author chain C； PDBConstruct 4–280； UniProt 2–278 Author chain D； PDBConstruct 4–280； UniProt 2–278 Author chain E； PDBConstruct 4–280； UniProt 2–278 Author chain F； PDBConstruct 4–280； UniProt 2–278

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1x8m
Deposition date deposition_date	2004-08-18
Structure title title	X-ray structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from Escherichia coli
Keywords keywords	;Structural genomics, protein structure initiative, 5-keto 4-deoxyuronate isomerase, NYSGXRC target T1827, PSI, New York SGX Research Center for Structural Genomics, ISOMERASE ;; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	42.56 Å
Radius of gyration Rg (electron density) rg_electron	42.45 Å
Forward intensity I(0) i0	442150000.00
Molecular weight molecular_weight	172400.0 kDa
Excluded volume excluded_volume	215520 Å³
Envelope volume envelope_volume	283700 Å³
Hydration-shell volume shell_volume	57018 Å³
Envelope diameter envelope_diameter	157.7 Å
Shell Rg shell_rg	46.14 Å
Envelope Rg envelope_rg	42.22 Å
Shape Rg shape_rg	42.44 Å
Total Rg total_rg	42.70 Å
Total atoms total_atoms	12126
Residues n_residues	1554
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

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

Maximum dimension Dmax dmax	151.2 Å
Rg (real space) rg_real	42.79 Å
Rg uncertainty (real space) rg_real_error	1.60 Å
I(0) (real space) i0_real	4.4210e+08
I(0) uncertainty (real space) i0_real_error	8.5440e+06
Rg (reciprocal space) rg_reciprocal	42.56 Å
I(0) (reciprocal space) i0_reciprocal	442000000.0000
Solution quality estimate total_estimate	0.8463
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	49.0 Å
Skewness Skewness skewness	0.522
Kurtosis Kurtosis kurtosis	-0.091
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	75720000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.783

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1x8ma1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.13 — KduI-like

Domain ID domain_id	d1x8ma2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1x8mb1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.13 — KduI-like

Domain ID domain_id	d1x8mb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1x8mc1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.13 — KduI-like

Domain ID domain_id	d1x8mc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1x8md1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.13 — KduI-like

Domain ID domain_id	d1x8md2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1x8me1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.13 — KduI-like

Domain ID domain_id	d1x8me2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1x8mf1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.13 — KduI-like

Domain ID domain_id	d1x8mf2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (12 domains)

Domain ID domain_id	1x8mA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	520 — pectin degrading enzyme 5-keto 4- deoxyuronate isomerase, domain 1

Domain ID domain_id	1x8mA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	1x8mB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	520 — pectin degrading enzyme 5-keto 4- deoxyuronate isomerase, domain 1

Domain ID domain_id	1x8mB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	1x8mC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	520 — pectin degrading enzyme 5-keto 4- deoxyuronate isomerase, domain 1

Domain ID domain_id	1x8mC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	1x8mD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	520 — pectin degrading enzyme 5-keto 4- deoxyuronate isomerase, domain 1

Domain ID domain_id	1x8mD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	1x8mE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	520 — pectin degrading enzyme 5-keto 4- deoxyuronate isomerase, domain 1

Domain ID domain_id	1x8mE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	1x8mF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	520 — pectin degrading enzyme 5-keto 4- deoxyuronate isomerase, domain 1

Domain ID domain_id	1x8mF02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

▶

8. Citations (1)

▶

Unit-cell length a length_a	101.011 Å
Unit-cell length b length_b	101.011 Å
Unit-cell length c length_c	179.410 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2590
R_work r_work	0.2570
R_free r_free	0.2800

Description description	4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
Molecular weight formula_weight	32327.6 kDa
EC 编号 ec_number	5.3.1.17
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	12126

X-ray structure of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase from Escherichia coli

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

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

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/x8/1x8m/1x8m.fit
pddf	/app/data/pr_computation/x8/1x8m/1x8m.pr.out
profile	/app/data/saxs_computation/x8/1x8m/1x8m.dat