SAXSdb — 1qt1

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

PROTEIN (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 2–388 Chain B； UniProt 2–388	Not recorded	CO COBALT (II) ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 1.85 Å R-free 0.219

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 1QT1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CLK CRYSTAL STRUCTURE OF STREPTOMYCES DIASTATICUS NO.7 STRAIN M1033 XYLOSE ISOMERASE AT 1.9 A RESOLUTION WITH PSEUDO-I222 SPACE GROUP Deposited 1999-04-29	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–388（387 aa）	Not recorded	MG MAGNESIUM ION × 4 CO COBALT (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	XYLA_STRDI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–387； UniProt 2–388 Author chain B； PDBConstruct 1–387； UniProt 2–388

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	1qt1
Deposition date deposition_date	1999-06-29
Structure title title	CRYSTAL STRUCTURE OF XYLOSE ISOMERASE FROM STREPTOMYCES DIASTATICUS NO.7 M1033 AT 1.85 A RESOLUTION
Keywords keywords	ISOMERASE, XYLOSE ISOMERASE, GLUCOSE ISOMERASE, STREPTOMYCES, TRUE SPACE GROUP; 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	31.10 Å
Radius of gyration Rg (electron density) rg_electron	30.01 Å
Forward intensity I(0) i0	123820000.00
Molecular weight molecular_weight	85315.0 kDa
Excluded volume excluded_volume	105570 Å³
Envelope volume envelope_volume	145810 Å³
Hydration-shell volume shell_volume	39578 Å³
Envelope diameter envelope_diameter	104.0 Å
Shell Rg shell_rg	37.78 Å
Envelope Rg envelope_rg	30.64 Å
Shape Rg shape_rg	30.01 Å
Total Rg total_rg	30.72 Å
Total atoms total_atoms	6022
Residues n_residues	774
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	99.4 Å
Rg (real space) rg_real	31.03 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.2380e+08
I(0) uncertainty (real space) i0_real_error	1.5630e+06
Rg (reciprocal space) rg_reciprocal	31.06 Å
I(0) (reciprocal space) i0_reciprocal	123800000.0000
Solution quality estimate total_estimate	0.8970
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.1 Å
Skewness Skewness skewness	0.232
Kurtosis Kurtosis kurtosis	-0.496
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30980000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.886

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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	PROTEIN (XYLOSE ISOMERASE)
Molecular weight formula_weight	42695.6 kDa
EC 编号 ec_number	5.3.1.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6658

SYQPTPEDKFTFGLWTVGWQGRDPFGDATRGALDPAESVRRLAELGAHGVTFHDDDLIPFGATDSERAEHIKRFRQGLDETGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAQTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVTSQGYDTPFAIEPKPNEPRGDILLPTIGHALAFIDGLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGPGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRAARLDELAQPTAGDGLQALLPDRSAFEDFDPDAAAARGMAFERLDQLAMDHLLGARG

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	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	636

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1qt1a_
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	d1qt1b_
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	1qt1A00
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	1qt1B00
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	87.976 Å
Unit-cell length b length_b	98.836 Å
Unit-cell length c length_c	93.927 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	5.000 Å
R factor r_factor	0.1660
R_work r_work	0.1660
R_free r_free	0.2190

fit	/app/data/saxs_computation/qt/1qt1/1qt1.fit
pddf	/app/data/pr_computation/qt/1qt1/1qt1.pr.out
profile	/app/data/saxs_computation/qt/1qt1/1qt1.dat

CRYSTAL STRUCTURE OF XYLOSE ISOMERASE FROM STREPTOMYCES DIASTATICUS NO.7 M1033 AT 1.85 A RESOLUTION

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

PROTEIN (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