SAXSdb — 1a0e

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

XYLOSE ISOMERASE

Thermotoga neapolitana

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 2–444 Chain D； UniProt 2–444	Not recorded	CO COBALT (II) ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；PROTEIN WAS CRYSTALLIZED FROM 14% JEFFAMINE ED 4000, 5 MM MGSO4, 0.5 MM COCL2, 50 MM MOPS, PH 7.0 (FOR DETAILS SEE REFERENCE 1).	Resolution 2.70 Å R-free 0.203

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_THENE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–443； UniProt 2–444 Author chain D； PDBConstruct 1–443； UniProt 2–444

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	1a0e
Deposition date deposition_date	1997-11-28
Structure title title	XYLOSE ISOMERASE FROM THERMOTOGA NEAPOLITANA
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	31.79 Å
Radius of gyration Rg (electron density) rg_electron	30.81 Å
Forward intensity I(0) i0	147451000.00
Molecular weight molecular_weight	99310.0 kDa
Excluded volume excluded_volume	125170 Å³
Envelope volume envelope_volume	163200 Å³
Hydration-shell volume shell_volume	43298 Å³
Envelope diameter envelope_diameter	105.4 Å
Shell Rg shell_rg	38.64 Å
Envelope Rg envelope_rg	30.73 Å
Shape Rg shape_rg	30.79 Å
Total Rg total_rg	31.56 Å
Total atoms total_atoms	7018
Residues n_residues	886
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	101.6 Å
Rg (real space) rg_real	31.69 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	1.4750e+08
I(0) uncertainty (real space) i0_real_error	2.2690e+06
Rg (reciprocal space) rg_reciprocal	31.74 Å
I(0) (reciprocal space) i0_reciprocal	147500000.0000
Solution quality estimate total_estimate	0.9027
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.5 Å
Skewness Skewness skewness	0.214
Kurtosis Kurtosis kurtosis	-0.565
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	66180000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.961

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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	50831.6 kDa
EC 编号 ec_number	5.3.1.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	7274

AEFFPEIPKVQFEGKESTNPLAFKFYDPEEIIDGKPLKDHLKFSVAFWHTFVNEGRDPFGDPTADRPWNRYTDPMDKAFARVDALFEFCEKLNIEYFCFHDRDIAPEGKTLRETNKILDKVVERIKERMKDSNVKLLWGTANLFSHPRYMHGAATTCSADVFAYAAAQVKKALEITKELGGEGYVFWGGREGYETLLNTDLGFELENLARFLRMAVDYAKRIGFTGQFLIEPKPKEPTKHQYDFDVATAYAFLKSHGLDEYFKFNIEANHATLAGHTFQHELRMARILGKLGSIDANQGDLLLGWDTDQFPTNVYDTTLAMYEVIKAGGFTKGGLNFDAKVRRASYKVEDLFIGHIAGMDTFALGFKVAYKLVKDGVLDKFIEEKYRSFREGIGRDIVEGKVDFEKLEEYIIDKETIELPSGKQEYLESLINSYIVKTILELR

来源 Source

来源生物 organism	Thermotoga neapolitana
NCBI Class编号 ncbi_taxonomy_id	2337
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	256

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1a0ea_
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	d1a0ed_
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 (2 domains)

Domain ID domain_id	1a0eA00
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	1a0eD00
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 (3)

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Unit-cell length a length_a	161.790 Å
Unit-cell length b length_b	121.870 Å
Unit-cell length c length_c	98.860 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	12.500 Å
R factor r_factor	0.1800
R_work r_work	0.1800
R_free r_free	0.2030

fit	/app/data/saxs_computation/a0/1a0e/1a0e.fit
pddf	/app/data/pr_computation/a0/1a0e/1a0e.pr.out
profile	/app/data/saxs_computation/a0/1a0e/1a0e.dat

XYLOSE ISOMERASE FROM THERMOTOGA NEAPOLITANA

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