SAXSdb — 1a0d

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

XYLOSE ISOMERASE

OrganismNot specified

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 2–441 Chain B； UniProt 2–441 Chain C； UniProt 2–441 Chain D； UniProt 2–441	Not recorded	MN MANGANESE (II) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；VAPOR DIFFUSION FROM HANGING DROPS (18 DEG C): PROTEIN (A280 22) WAS IN 50 MM TRIS, 10 MM MNCL2, PH 7.5; RESERVOIR SOLUTION WAS 10% PEG, 100 MM LICL, 100 MM MES, PH 6.3; DROPS WERE FORMED FROM EQUAL PARTS OF PROTEIN AND RESERVOIR SOLUTIONS., pH 6.5, vapor diffusion - hanging drop	Resolution 3.00 Å R-free 0.209

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	XYLA_BACST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–440； UniProt 2–441 Author chain B； PDBConstruct 1–440； UniProt 2–441 Author chain C； PDBConstruct 1–440； UniProt 2–441 Author chain D； PDBConstruct 1–440； UniProt 2–441

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1a0d
Deposition date deposition_date	1997-11-28
Structure title title	XYLOSE ISOMERASE FROM BACILLUS STEAROTHERMOPHILUS
Keywords keywords	;KETOLISOMERASE, XYLOSE METABOLISM, GLUCOSE-FRUCTOSE INTERCONVERSION, HYDRIDE TRANSFER, ALPHA-BETA BARREL, METALLOENZYME, THERMOPHILE ;; KETOLISOMERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	34.49 Å
Radius of gyration Rg (electron density) rg_electron	33.56 Å
Forward intensity I(0) i0	582190000.00
Molecular weight molecular_weight	197960.0 kDa
Excluded volume excluded_volume	247780 Å³
Envelope volume envelope_volume	294090 Å³
Hydration-shell volume shell_volume	67527 Å³
Envelope diameter envelope_diameter	102.0 Å
Shell Rg shell_rg	43.97 Å
Envelope Rg envelope_rg	33.44 Å
Shape Rg shape_rg	33.55 Å
Total Rg total_rg	34.27 Å
Total atoms total_atoms	13980
Residues n_residues	1748
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

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

Maximum dimension Dmax dmax	102.7 Å
Rg (real space) rg_real	34.23 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	5.8220e+08
I(0) uncertainty (real space) i0_real_error	8.3600e+06
Rg (reciprocal space) rg_reciprocal	34.40 Å
I(0) (reciprocal space) i0_reciprocal	582300000.0000
Solution quality estimate total_estimate	0.8991
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	46.9 Å
Skewness Skewness skewness	0.042
Kurtosis Kurtosis kurtosis	-0.544
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	479000000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.942

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	XYLOSE ISOMERASE
Molecular weight formula_weight	50073.4 kDa
EC 编号 ec_number	5.3.1.5
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	14220

PYFDNISTIAYEGPASKNPLAFKFYNPEEKVGDKTMEEHLRFSVAYWHTFTGDGSDPFGAGNMIRPWNKYSGMDLAKARVEAAFEFFEKLNIPFFCFHDVDIAPEGETLKETYKNLDIIVDMIEEYMKTSKTKLLWNTANLFTHPRFVHGAATSCNADVFAYAAAKVKKGLEIAKRLGAENYVFWGGREGYETLLNTDMKLELDNLARFLHMAVDYAKEIGFDGQFLIEPKPKEPTKHQYDFDVATALAFLQTYGLKDYFKFNIEANHATLAGHTFEHELRVARIHGMLGSVDANQGDMLLGWDTDEFPTDLYSTTLAMYEILKNGGLGRGGLNFDAKVRRGSFEPEDLFYAHIAGMDSFAVGLKVAHRLIEDRVFDEFIEERYKSYTEGIGREIVEGTADFHKLEAHALQLGEIQNQSGRQERLKTLLNQYLLEVCAAR

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	240

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1a0da_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.15 — Xylose isomerase-like
Family Family family	c.1.15.3 — Xylose isomerase

Domain ID domain_id	d1a0db_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.15 — Xylose isomerase-like
Family Family family	c.1.15.3 — Xylose isomerase

Domain ID domain_id	d1a0dc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.15 — Xylose isomerase-like
Family Family family	c.1.15.3 — Xylose isomerase

Domain ID domain_id	d1a0dd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.15 — Xylose isomerase-like
Family Family family	c.1.15.3 — Xylose isomerase

CATH v4.4 (4 domains)

Domain ID domain_id	1a0dA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

Domain ID domain_id	1a0dB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

Domain ID domain_id	1a0dC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

Domain ID domain_id	1a0dD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

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8. Citations (2)

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Unit-cell length a length_a	86.290 Å
Unit-cell length b length_b	141.850 Å
Unit-cell length c length_c	160.660 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1930
R_work r_work	0.1930
R_free r_free	0.2090

fit	/app/data/saxs_computation/a0/1a0d/1a0d.fit
pddf	/app/data/pr_computation/a0/1a0d/1a0d.pr.out
profile	/app/data/saxs_computation/a0/1a0d/1a0d.dat

XYLOSE ISOMERASE FROM BACILLUS STEAROTHERMOPHILUS

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

XYLOSE 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

Diffraction experiment Diffraction