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1clk

CRYSTAL STRUCTURE OF STREPTOMYCES DIASTATICUS NO.7 STRAIN M1033 XYLOSE ISOMERASE AT 1.9 A RESOLUTION WITH PSEUDO-I222 SPACE GROUP

Method: X-RAY DIFFRACTION Dmax: 85.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

XYLOSE ISOMERASE

OrganismNot specified

UniProt P50910

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 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

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 1CLK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1QT1 CRYSTAL STRUCTURE OF XYLOSE ISOMERASE FROM STREPTOMYCES DIASTATICUS NO.7 M1033 AT 1.85 A RESOLUTION Deposited 1999-06-29 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）
Chain B 2–388（387 aa）
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

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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1clk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1clk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1clk
Deposition date deposition_date1999-04-29
Structure title titleCRYSTAL STRUCTURE OF STREPTOMYCES DIASTATICUS NO.7 STRAIN M1033 XYLOSE ISOMERASE AT 1.9 A RESOLUTION WITH PSEUDO-I222 SPACE GROUP
Keywords keywordsISOMERASE, XYLOSE ISOMERASE, GLUCOSE ISOMERASE, STREPTOMYCES, PSEUDO-I222; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.56 Å
Radius of gyration Rg (electron density) rg_electron23.43 Å
Forward intensity I(0) i032716100.00
Molecular weight molecular_weight42637.0 kDa
Excluded volume excluded_volume52799 ų
Envelope volume envelope_volume68767 ų
Hydration-shell volume shell_volume24957 ų
Envelope diameter envelope_diameter88.8 Å
Shell Rg shell_rg29.74 Å
Envelope Rg envelope_rg24.47 Å
Shape Rg shape_rg23.42 Å
Total Rg total_rg24.23 Å
Total atoms total_atoms3012
Residues n_residues387
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax85.7 Å
Rg (real space) rg_real24.66 Å
Rg uncertainty (real space) rg_real_error0.90 Å
I(0) (real space) i0_real3.2720e+07
I(0) uncertainty (real space) i0_real_error5.1210e+05
Rg (reciprocal space) rg_reciprocal24.64 Å
I(0) (reciprocal space) i0_reciprocal32720000.0000
Solution quality estimate total_estimate0.8488
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.2 Å
Skewness Skewness skewness0.498
Kurtosis Kurtosis kurtosis-0.095
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5862000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.721; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.884; Smooth: 0.984
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1clka_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.15 — Xylose isomerase-like
Family Family familyc.1.15.3 — Xylose isomerase

CATH v4.4 (1 domains)

Domain ID domain_id1clkA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily150 — Divalent-metal-dependent TIM barrel enzymes
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8. Citations (3)

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9. Files and Curves (10)