SAXSdb — 9xim

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

D-XYLOSE ISOMERASE

Actinoplanes missouriensis

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 1–393 Chain B； UniProt 1–393 Chain C； UniProt 1–393 Chain D； UniProt 1–393	Not recorded	XLS D-xylose × 4 MN MANGANESE (II) ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.40 Å

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 9XIM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BHW LOW TEMPERATURE MIDDLE RESOLUTION STRUCTURE OF XYLOSE ISOMERASE FROM MASC DATA Deposited 1998-06-10	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 1–393（393 aa） Chain B 1–393（393 aa） Chain C 1–393（393 aa） Chain D 1–393（393 aa）	Mutation：H220N Mutation：H220N Mutation：H220N Mutation：H220N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULPHATE	Resolution 4.10 Å R-free 0.321
1XIM ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS Deposited 1991-05-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–393（393 aa） Chain B 1–393（393 aa） Chain C 1–393（393 aa） Chain D 1–393（393 aa）	Not recorded	XYL Xylitol × 4 CO COBALT (II) ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1XIN PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES Deposited 1992-04-06	Different ligand/ion	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–393（393 aa） Chain B 1–393（393 aa） Chain C 1–393（393 aa） Chain D 1–393（393 aa）	Not recorded	XYL Xylitol × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
2XIM ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS Deposited 1991-05-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–393（393 aa） Chain B 1–393（393 aa） Chain C 1–393（393 aa） Chain D 1–393（393 aa）	Not recorded	XYL Xylitol × 4 MG MAGNESIUM ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
2XIN PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES Deposited 1992-04-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–393（393 aa） Chain B 1–393（393 aa） Chain C 1–393（393 aa） Chain D 1–393（393 aa）	Not recorded	SOR sorbitol × 4 CO COBALT (II) ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
3XIM ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS Deposited 1991-05-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–393（393 aa） Chain B 1–393（393 aa） Chain C 1–393（393 aa） Chain D 1–393（393 aa）	Not recorded	SOR sorbitol × 4 CO COBALT (II) ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
3XIN PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES Deposited 1992-04-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–393（393 aa） Chain B 1–393（393 aa） Chain C 1–393（393 aa） Chain D 1–393（393 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
4XIM PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES Deposited 1992-03-11	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–393（393 aa） Chain B 1–393（393 aa） Chain C 1–393（393 aa） Chain D 1–393（393 aa）	Not recorded	CO COBALT (II) ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
5XIM PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES Deposited 1992-03-30	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–393（393 aa） Chain B 1–393（393 aa） Chain C 1–393（393 aa） Chain D 1–393（393 aa）	Not recorded	SOR sorbitol × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
5XIN PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES Deposited 1992-04-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–393（393 aa） Chain B 1–393（393 aa） Chain C 1–393（393 aa） Chain D 1–393（393 aa）	Not recorded	XLS D-xylose × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
6XIM PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES Deposited 1992-04-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–393（393 aa） Chain B 1–393（393 aa） Chain C 1–393（393 aa） Chain D 1–393（393 aa）	Not recorded	XLS D-xylose × 4 MG MAGNESIUM ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
7XIM PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES Deposited 1992-04-03	Different ligand/ion	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–393（393 aa） Chain B 1–393（393 aa） Chain C 1–393（393 aa） Chain D 1–393（393 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
8XIM PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES Deposited 1992-04-01	Different ligand/ion	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–393（393 aa） Chain B 1–393（393 aa） Chain C 1–393（393 aa） Chain D 1–393（393 aa）	Not recorded	XLS D-xylose × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	XYLA_ACTMI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–393； UniProt 1–393 Author chain B； PDBConstruct 1–393； UniProt 1–393 Author chain C； PDBConstruct 1–393； UniProt 1–393 Author chain D； PDBConstruct 1–393； UniProt 1–393

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	9xim
Deposition date deposition_date	1992-04-03
Structure title title	PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES
Keywords keywords	ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE); ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
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	32.84 Å
Radius of gyration Rg (electron density) rg_electron	31.79 Å
Forward intensity I(0) i0	463850000.00
Molecular weight molecular_weight	173110.0 kDa
Excluded volume excluded_volume	216070 Å³
Envelope volume envelope_volume	250440 Å³
Hydration-shell volume shell_volume	60816 Å³
Envelope diameter envelope_diameter	102.7 Å
Shell Rg shell_rg	41.77 Å
Envelope Rg envelope_rg	31.94 Å
Shape Rg shape_rg	31.78 Å
Total Rg total_rg	32.52 Å
Total atoms total_atoms	12236
Residues n_residues	1567
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	100.9 Å
Rg (real space) rg_real	32.55 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	4.6380e+08
I(0) uncertainty (real space) i0_real_error	6.7100e+06
Rg (reciprocal space) rg_reciprocal	32.68 Å
I(0) (reciprocal space) i0_reciprocal	463900000.0000
Solution quality estimate total_estimate	0.8898
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.0 Å
Skewness Skewness skewness	0.112
Kurtosis Kurtosis kurtosis	-0.448
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	592100000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.926

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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	43420.5 kDa
EC 编号 ec_number	5.3.1.5
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	13214

SVQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIGAYGITFHDDDLVPFGSDAQTRDGIIAGFKKALDETGLIVPMVTTNLFTHPVFKDGGFTSNDRSVRRYAIRKVLRQMDLGAELGAKTLVLWGGREGAEYDSAKDVSAALDRYREALNLLAQYSEDRGYGLRFAIEPKPNQPRGDILLPTAGHAIAFVQELERPELFGINPETGHEQMSNLNFTQGIAQALWHKKLFHIDLNGQHGPKFDQDLVFGHGDLLNAFSLVDLLENGPDGAPAYDGPRHFDYKPSRTEDYDGVWESAKANIRMYLLLKERAKAFRADPEVQEALAASKVAELKTPTLNPGEGYAELLADRSAFEDYDADAVGAKGFGFVKLNQLAIEHLLGAR

来源 Source

来源生物 organism	Actinoplanes missouriensis
NCBI Class编号 ncbi_taxonomy_id	1866

Entity 2 Entity 2 non-polymer

Description description	D-xylose
Molecular weight formula_weight	150.1 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 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 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	978

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d9xima_
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	d9ximb_
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	d9ximc_
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	d9ximd_
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	9ximA00
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	9ximB00
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	9ximC00
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	9ximD00
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 (5)

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Unit-cell length a length_a	143.450 Å
Unit-cell length b length_b	143.450 Å
Unit-cell length c length_c	231.500 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	24

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1440
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/xi/9xim/9xim.fit
pddf	/app/data/pr_computation/xi/9xim/9xim.pr.out
profile	/app/data/saxs_computation/xi/9xim/9xim.dat

PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES