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1c7t

BETA-N-ACETYLHEXOSAMINIDASE MUTANT E540D COMPLEXED WITH DI-N ACETYL-D-GLUCOSAMINE (CHITOBIASE)

Method: X-RAY DIFFRACTION Dmax: 90.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

BETA-N-ACETYLHEXOSAMINIDASE

Serratia marcescens

UniProt Q54468

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 Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 28–885 Fragment：MATURE PROTEIN, PERIPLASMATIC TARGETING SEQUENCE RESIDUES 1-27 CLEAVED OFF DURING MATURATION Mutation：YES 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.8；CO-CRYSTALS WERE GROWN BY THE HANGING-DROP VAPOR DIFFUSION METHOD. RESERVOIR BUFFER CONTAINED 2.3 MOLAR AMMONIUM SULFATE AND 100 MILLIMOLAR CACODYLATE BUFFER PH 4.8. PROTEIN SOLUTION 40 MILLIGRAM PER MILLILITER WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR CONTAINING 10 MILLIMOLAR DI-NAG. CRYSTALS ABOUT 0.5 X 0.2 X 0.2 MILLIMETER IN SIZE WERE FORMED WITHIN 2-3 DAYS., VAPOR DIFFUSION, HANGING DROP Resolution 1.90 Å R-free 0.246

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 1C7T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C7S BETA-N-ACETYLHEXOSAMINIDASE MUTANT D539A COMPLEXED WITH DI-N-ACETYL-BETA-D-GLUCOSAMINE (CHITOBIASE) Deposited 2000-03-14 Different mutation/modification Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–885（858 aa） Fragment：MATURE PROTEIN, PERIPLASMATIC TARGETING SEQUENCE RESIDUES 1-27 CLEAVED OFF DURING MATURATION
Mutation：D539A SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；CO-CRYSTALS WERE GROWN BY THE HANGING-DROP VAPOR DIFFUSION METHOD. RESERVOIR BUFFER CONTAINED 2.3 MOLAR AMMONIUM SULFATE AND 100 MILLIMOLAR CACODYLATE BUFFER PH 4.8. PROTEIN SOLUTION 40 MILLIGRAM PER MILLILITER WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR CONTAINING 10 MILLIMOLAR DI-NAG. CRYSTALS ABOUT 0.5 X 0.2 X 0.2 MILLIMETER IN SIZE WERE FORMED WITHIN 2-3 DAYS., VAPOR DIFFUSION, HANGING DROP
Resolution 1.80 Å R-free 0.224
1QBA BACTERIAL CHITOBIASE, GLYCOSYL HYDROLASE FAMILY 20 Deposited 1996-06-06 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 28–885（858 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；CRYSTAL WERE GROWN AT ROOM TEMPERATURE FROM HANGING DROPS CONTAINING 62% SATURATED AMMONIUM SULFATE, 1.5% ISOPROPANOL AND 100 MM CACODYLATE, PH 5.6., vapor diffusion - hanging drop
Resolution 1.85 Å R-free 0.196
1QBB BACTERIAL CHITOBIASE COMPLEXED WITH CHITOBIOSE (DINAG) Deposited 1996-06-07 Different construct 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 28–885（858 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；CRYSTAL WERE GROWN AT ROOM TEMPERATURE FROM HANGING DROPS CONTAINING 62% SATURATED AMMONIUM SULFATE, 1.5% ISOPROPANOL AND 100 MM CACODYLATE, PH 5.6. DERIVATIZATION CONDITIONS: SOLID CHITOBIOSE WAS ADDED TO THE MOTHER LIQUOR TO MAKE UP HIGH CONCENTRATED STOCK SOLUTION, 0.5 TO 1.0 MICRO LITERS OF THE STOCK SOLUTION WERE ADDED TO THE CRYSTALLISATION DROP CONTAINING CRYSTALS. THE CRYSTALS WERE MOUNTED IMMEDIATELY IN GLASS CAPILLARY. EXPOSURE TIME WAS LIMITED TO 10 MINUTES OR LESS. THESE CRYSTALS: 4 MINS 50 SECS. THE CHITOBIOSE WAS SUPPLIED BY SIGMA., vapor diffusion - hanging drop
Resolution 2.00 Å R-free 0.212

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CHB_SERMA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–858； UniProt 28–885

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 1c7t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1c7t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1c7t
Deposition date deposition_date2000-03-17
Structure title titleBETA-N-ACETYLHEXOSAMINIDASE MUTANT E540D COMPLEXED WITH DI-N ACETYL-D-GLUCOSAMINE (CHITOBIASE)
Keywords keywords;GLYCOSYL HYDROLASE, BETA-N-ACETYLHEXOSAMINIDASE, CHITINOLYSIN, A/B(TIM)-BARREL, SITE DIRECTED MUTAGENESIS, PROTON DONOR, CO-CRYSTAL STRUCTURE, 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_guinier28.54 Å
Radius of gyration Rg (electron density) rg_electron27.61 Å
Forward intensity I(0) i0153008000.00
Molecular weight molecular_weight96652.0 kDa
Excluded volume excluded_volume120210 ų
Envelope volume envelope_volume138700 ų
Hydration-shell volume shell_volume40317 ų
Envelope diameter envelope_diameter95.8 Å
Shell Rg shell_rg36.22 Å
Envelope Rg envelope_rg27.96 Å
Shape Rg shape_rg27.56 Å
Total Rg total_rg28.55 Å
Total atoms total_atoms6818
Residues n_residues858
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 dmax90.2 Å
Rg (real space) rg_real28.43 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real1.5300e+08
I(0) uncertainty (real space) i0_real_error2.4880e+06
Rg (reciprocal space) rg_reciprocal28.48 Å
I(0) (reciprocal space) i0_reciprocal153000000.0000
Solution quality estimate total_estimate0.8968
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.5 Å
Skewness Skewness skewness0.220
Kurtosis Kurtosis kurtosis-0.393
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha31030000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.966
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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1c7ta1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.2 — E-set domains of sugar-utilizing enzymes
Domain ID domain_idd1c7ta2
Class classb — All beta proteins
Fold Fold foldb.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamilyb.2.2 — Carbohydrate-binding domain
Family Family familyb.2.2.3 — Bacterial chitobiase, n-terminal domain
Domain ID domain_idd1c7ta3
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.1.8.6 — beta-N-acetylhexosaminidase catalytic domain
Domain ID domain_idd1c7ta4
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.2 — beta-N-acetylhexosaminidase-like domain
Family Family familyd.92.2.1 — beta-N-acetylhexosaminidase domain

CATH v4.4 (4 domains)

Domain ID domain_id1c7tA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily290 —
Domain ID domain_id1c7tA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology379 — Chitobiase; domain 2
Homologous superfamily homologous superfamily10 — Chitobiase/beta-hexosaminidase domain 2-like
Domain ID domain_id1c7tA03
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1c7tA04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (3)

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9. Files and Curves (10)