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5jiw

Crystal structure of Thermus aquaticus amylomaltase (GH77) in complex with a 34-meric cycloamylose

Method: X-RAY DIFFRACTION Dmax: 78.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

4-alpha-glucanotransferase

Thermus aquaticus

UniProt O87172

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–500 Mutation：D293A,D395N Non-standard monomer：Yes (specific site not provided by mmCIF) ;alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose ; × 1 EDO 1,2-ETHANEDIOL × 2 CO3 CARBONATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1.0 M NaKphosphate pH 7 Resolution 1.73 Å R-free 0.188

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 5JIW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CWY CRYSTAL STRUCTURE OF AMYLOMALTASE FROM THERMUS AQUATICUS, A GLYCOSYLTRANSFERASE CATALYSING THE PRODUCTION OF LARGE CYCLIC GLUCANS Deposited 1999-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–500（500 aa） Fragment：MALQ
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 8000, ETHYLENE GLYCOL, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.00 Å R-free 0.222
1ESW X-RAY STRUCTURE OF ACARBOSE BOUND TO AMYLOMALTASE FROM THERMUS AQUATICUS. IMPLICATIONS FOR THE SYNTHESIS OF LARGE CYCLIC GLUCANS Deposited 2000-04-11 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–500（500 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；Bicine, PEG 8000, Ethylene glycol, NaCl , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.90 Å R-free 0.219
1FP8 STRUCTURE OF THE AMYLOMALTASE FROM THERMUS THERMOPHILUS HB8 IN SPACE GROUP P21212 Deposited 2000-08-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–500（500 aa）
Not recorded HG MERCURY (II) ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；12% PEG 20000, 100 mM MES (2-N-morpholino- ethanesulfonic acid) buffer, 3 mM HgCl2, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.232
1FP9 STRUCTURE OF AMYLOMALTASE FROM THERMUS THERMOPHILUS HB8 IN SPACE GROUP C2 Deposited 2000-08-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–500（500 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；12% PEG 20000, 100 mM maleate buffer, 0.1% (w/v) maltotriose, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.10 Å R-free 0.290
9U5L 4-alpha-glucanotransferase from Thermus thermophilus STB20 Deposited 2025-03-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–500（500 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293.15 K；0.1M Bis-Tris pH 5.5, 35% PEG 3350
Resolution 2.10 Å R-free 0.316

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MALQ_THETH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–500； UniProt 1–500

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 5jiw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5jiw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5jiw
Deposition date deposition_date2016-04-22
Structure title titleCrystal structure of Thermus aquaticus amylomaltase (GH77) in complex with a 34-meric cycloamylose
Keywords keywordsglycoside hydrolase, TIM barrel cycloamylose, Hydrolase; HYDROLASE
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_guinier24.40 Å
Radius of gyration Rg (electron density) rg_electron23.07 Å
Forward intensity I(0) i056807900.00
Molecular weight molecular_weight60153.0 kDa
Excluded volume excluded_volume75743 ų
Envelope volume envelope_volume87317 ų
Hydration-shell volume shell_volume30570 ų
Envelope diameter envelope_diameter84.3 Å
Shell Rg shell_rg31.09 Å
Envelope Rg envelope_rg23.26 Å
Shape Rg shape_rg23.04 Å
Total Rg total_rg24.07 Å
Total atoms total_atoms8348
Residues n_residues498
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 dmax78.7 Å
Rg (real space) rg_real24.26 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real5.6810e+07
I(0) uncertainty (real space) i0_real_error7.5650e+05
Rg (reciprocal space) rg_reciprocal24.29 Å
I(0) (reciprocal space) i0_reciprocal56810000.0000
Solution quality estimate total_estimate0.8882
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.0 Å
Skewness Skewness skewness0.200
Kurtosis Kurtosis kurtosis-0.377
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15290000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.978
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5jiwa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.1 — Amylase, catalytic domain

CATH v4.4 (1 domains)

Domain ID domain_id5jiwA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
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8. Citations (1)

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9. Files and Curves (10)