SAXSdb — 1xlm

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

D-XYLOSE ISOMERASE

Arthrobacter sp. NRRL

UniProt P12070

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 1–394 Chain B； UniProt 1–394	Mutation：D254E, D256E	XYL Xylitol × 4 AL ALUMINUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；PROTEIN WAS CRYSTALLIZED FROM 0.75 M (NH4)2SO4, 1.50 MM THYMOL, 0.05 TRIS, PH 7.0, THEN SOAKED INTO A SOLUTION CONTAINING 5 MM AL3+, 1.5 M XYLITOL, 1.50 M (NH4)2SO4 AND 6.0 M THYMOL IN 1.50 M TRIS-HCL PH 8.0 FOR TWO DAYS	Resolution 2.40 Å R-free 0.222

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 1XLM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DID OBSERVATIONS OF REACTION INTERMEDIATES AND THE MECHANISM OF ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE Deposited 1992-06-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	DIG 2,5-DIDEOXY-2,5-IMINO-D-GLUCITOL × 4 MN MANGANESE (II) ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1DIE OBSERVATIONS OF REACTION INTERMEDIATES AND THE MECHANISM OF ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE Deposited 1992-06-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 8 NOJ 1-DEOXYNOJIRIMYCIN × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1XLA MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT Deposited 1991-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1XLB MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT Deposited 1991-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1XLC MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT Deposited 1991-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	XYL Xylitol × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1XLD MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT Deposited 1991-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	XYL Xylitol × 4 MN MANGANESE (II) ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1XLE MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT Deposited 1991-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	MN MANGANESE (II) ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1XLF MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT Deposited 1991-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	GCO D-gluconic acid × 4 MN MANGANESE (II) ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1XLG MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT Deposited 1991-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	XYL Xylitol × 4 MG MAGNESIUM ION × 4 AL ALUMINUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1XLH MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT Deposited 1991-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	AL ALUMINUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1XLI MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT Deposited 1991-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	GLT 5-thio-alpha-D-glucopyranose × 4 MN MANGANESE (II) ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1XLJ MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT Deposited 1991-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	XYL Xylitol × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1XLK MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT Deposited 1991-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	MN MANGANESE (II) ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1XLL MECHANISM FOR ALDOSE-KETOSE INTERCONVERSION BY D-XYLOSE ISOMERASE INVOLVING RING OPENING FOLLOWED BY A 1,2-HYDRIDE SHIFT Deposited 1991-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa）	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
4XIA STRUCTURES OF D-XYLOSE ISOMERASE FROM ARTHROBACTER STRAIN B3728 CONTAINING THE INHIBITORS XYLITOL AND D-SORBITOL AT 2.5 ANGSTROMS AND 2.3 ANGSTROMS RESOLUTION, RESPECTIVELY Deposited 1989-07-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–394（393 aa） Chain B 2–394（393 aa）	Not recorded	SOR sorbitol × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
5XIA STRUCTURES OF D-XYLOSE ISOMERASE FROM ARTHROBACTER STRAIN B3728 CONTAINING THE INHIBITORS XYLITOL AND D-SORBITOL AT 2.5 ANGSTROMS AND 2.3 ANGSTROMS RESOLUTION, RESPECTIVELY Deposited 1989-07-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–394（393 aa） Chain B 2–394（393 aa）	Not recorded	XYL Xylitol × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	XYLA_ARTS7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–394； UniProt 1–394 Author chain B； PDBConstruct 1–394； UniProt 1–394

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	1xlm
Deposition date deposition_date	1997-07-22
Structure title title	D254E, D256E MUTANT OF D-XYLOSE ISOMERASE COMPLEXED WITH AL3 AND XYLITOL
Keywords keywords	ISOMERASE, AL, SUBSTRATE INDUCED METAL ION MOVEMENT, XYLOSE METABOLISM, PENTOSE SHUNT; ISOMERASE
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	30.75 Å
Radius of gyration Rg (electron density) rg_electron	29.75 Å
Forward intensity I(0) i0	122276000.00
Molecular weight molecular_weight	86571.0 kDa
Excluded volume excluded_volume	107770 Å³
Envelope volume envelope_volume	141870 Å³
Hydration-shell volume shell_volume	39359 Å³
Envelope diameter envelope_diameter	103.8 Å
Shell Rg shell_rg	37.47 Å
Envelope Rg envelope_rg	29.66 Å
Shape Rg shape_rg	29.73 Å
Total Rg total_rg	30.48 Å
Total atoms total_atoms	6116
Residues n_residues	786
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	96.8 Å
Rg (real space) rg_real	30.66 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	1.2230e+08
I(0) uncertainty (real space) i0_real_error	2.0500e+06
Rg (reciprocal space) rg_reciprocal	30.70 Å
I(0) (reciprocal space) i0_reciprocal	122300000.0000
Solution quality estimate total_estimate	0.6168
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.4 Å
Skewness Skewness skewness	0.227
Kurtosis Kurtosis kurtosis	-0.502
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	38470000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 0.998; Sysdev: 0.077; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	D-XYLOSE ISOMERASE
Molecular weight formula_weight	43237.2 kDa
EC 编号 ec_number	5.3.1.5
Mutation mutation	D254E, D256E
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6205

SVQPTPADHFTFGLWTVGWTGADPFGVATRKNLDPVEAVHKLAELGAYGITFHDNDLIPFDATEAEREKILGDFNQALKDTGLKVPMVTTNLFSHPVFKDGGFTSNDRSIRRFALAKVLHNIDLAAEMGAETFVMWGGREGSEYDGSKDLAAALDRMREGVDTAAGYIKDKGYNLRIALEPKPNEPRGDIFLPTVGHGLAFIEQLEHGDIVGLNPETGHEQMAGLNFTHGIAQALWAEKLFHIDLNGQRGIKYEQELVFGHGDLTSAFFTVDLLENGFPNGGPKYTGPRHFDYKPSRTDGYDGVWDSAKANMSMYLLLKERALAFRADPEVQEAMKTSGVFELGETTLNAGESAADLMNDSASFAGFDAEAAAERNFAFIRLNQLAIEHLLGSR

来源 Source

来源生物 organism	Arthrobacter sp. NRRL
NCBI Class编号 ncbi_taxonomy_id	1669
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	Xylitol
Molecular weight formula_weight	152.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ALUMINUM ION
Molecular weight formula_weight	27.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1xlma_
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	d1xlmb_
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	1xlmA00
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	1xlmB00
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	139.600 Å
Unit-cell length b length_b	140.700 Å
Unit-cell length c length_c	83.600 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 2
Space-group number int_tables_number	21
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1792
R_work r_work	0.1792
R_free r_free	0.2220

fit	/app/data/saxs_computation/xl/1xlm/1xlm.fit
pddf	/app/data/pr_computation/xl/1xlm/1xlm.pr.out
profile	/app/data/saxs_computation/xl/1xlm/1xlm.dat

D254E, D256E MUTANT OF D-XYLOSE ISOMERASE COMPLEXED WITH AL3 AND XYLITOL

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

D-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