SAXSdb — 1c7s

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

BETA-N-ACETYLHEXOSAMINIDASE

Serratia marcescens

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：D539A	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 1.80 Å R-free 0.224

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 1C7S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C7T BETA-N-ACETYLHEXOSAMINIDASE MUTANT E540D COMPLEXED WITH DI-N ACETYL-D-GLUCOSAMINE (CHITOBIASE) Deposited 2000-03-17	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：YES	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
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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1c7s
Deposition date deposition_date	2000-03-14
Structure title title	BETA-N-ACETYLHEXOSAMINIDASE MUTANT D539A COMPLEXED WITH DI-N-ACETYL-BETA-D-GLUCOSAMINE (CHITOBIASE)
Keywords keywords	;GLYCOSYL HYDROLASE, BETA-N-ACETYLHEXOSAMINIDASE, CHITINOLYSIS, A/B(TIM)-BARREL, SITE DIRECTED MUTAGENESIS, SUBSTRATE NUCLEOPHILE STABILIZER MUTATION, HYDROLASE ;; HYDROLASE
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	28.57 Å
Radius of gyration Rg (electron density) rg_electron	27.62 Å
Forward intensity I(0) i0	152427000.00
Molecular weight molecular_weight	96623.0 kDa
Excluded volume excluded_volume	120210 Å³
Envelope volume envelope_volume	139350 Å³
Hydration-shell volume shell_volume	40429 Å³
Envelope diameter envelope_diameter	94.8 Å
Shell Rg shell_rg	36.33 Å
Envelope Rg envelope_rg	28.01 Å
Shape Rg shape_rg	27.57 Å
Total Rg total_rg	28.56 Å
Total atoms total_atoms	6816
Residues n_residues	858
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	88.6 Å
Rg (real space) rg_real	28.45 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.5240e+08
I(0) uncertainty (real space) i0_real_error	2.0000e+06
Rg (reciprocal space) rg_reciprocal	28.50 Å
I(0) (reciprocal space) i0_reciprocal	152400000.0000
Solution quality estimate total_estimate	0.8999
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.8 Å
Skewness Skewness skewness	0.219
Kurtosis Kurtosis kurtosis	-0.397
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30410000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.941

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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	BETA-N-ACETYLHEXOSAMINIDASE
Molecular weight formula_weight	95940.9 kDa
EC 编号 ec_number	3.2.1.52
Mutation mutation	D539A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7656

DQQLVDQLSQLKLNVKMLDNRAGENGVDCAALGADWASCNRVLFTLSNDGQAIDGKDWVIYFHSPRQTLRVDNDQFKIAHLTGDLYKLEPTAKFSGFPAGKAVEIPVVAEYWQLFRNDFLPRWYATSGDAKPKMLANTDTENLDQFVAPFTGDQWKRTKDDKNILMTPASRFVSNADLQTLPAGALRGKIVPTPMQVKVHAQDADLRKGVALDLSTLVKPAADVVSQRFALLGVPVQTNGYPIKTDIQPGKFKGAMAVSGAYELKIGKKEAQVIGFDQAGVFYGLQSILSLVPSDGSGKIATLDASDAPRFPYRGIFLDVARNFHKKDAVLRLLDQMAAYKLNKFHFHLSDDEGWRIEIPGLPELTEVGGQRCHDLSETTCLLPQYGQGPDVYGGFFSRQDYIDIIKYAQARQIEVIPEIDMPAHARAAVVSMEARYKKLHAAGKEQEANEFRLVDQTDTSNTTSVQFFNRQSYLNPCLDSSQRFVDKVIGEIAQMHKEAGQPIKTWHFGGAEAKNIRLGAGYTDKAKPEPGKGIIDQSNEDKPWAKSQVCQTMIKEGKVADMEHLPSYFGQEVSKLVKAHGIDRMQAWQDGLKDAESSKAFATSRVGVNFWDTLYWGGFDSVNDWANKGYEVVVSNPDYVYMDFPYEVNPDERGYYWGTRFSDERKVFSFAPDNMPQNAETSVDRDGNHFNAKSDKPWPGAYGLSAQLWSETQRTDPQMEYMIFPRALSVAERSWHRAGWEQDYRAGREYKGGETHFVDTQALEKDWLRFANILGQRELAKLDKGGVAYRLPVPGARVAGGKLEANIALPGLGIEYSTDGGKQWQRYDAKAKPAVSGEVQVRSVSPDGKRYSRAEKV

来源 Source

来源生物 organism	Serratia marcescens
NCBI Class编号 ncbi_taxonomy_id	615
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	821

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1c7sa1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.2 — E-set domains of sugar-utilizing enzymes

Domain ID domain_id	d1c7sa2
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.2 — Carbohydrate-binding domain
Family Family family	b.2.2.3 — Bacterial chitobiase, n-terminal domain

Domain ID domain_id	d1c7sa3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.6 — beta-N-acetylhexosaminidase catalytic domain

Domain ID domain_id	d1c7sa4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.2 — beta-N-acetylhexosaminidase-like domain
Family Family family	d.92.2.1 — beta-N-acetylhexosaminidase domain

CATH v4.4 (4 domains)

Domain ID domain_id	1c7sA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	290 —

Domain ID domain_id	1c7sA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	379 — Chitobiase; domain 2
Homologous superfamily homologous superfamily	10 — Chitobiase/beta-hexosaminidase domain 2-like

Domain ID domain_id	1c7sA03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1c7sA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (2)

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Unit-cell length a length_a	108.794 Å
Unit-cell length b length_b	99.960 Å
Unit-cell length c length_c	86.308 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	4

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1830
R_work r_work	0.1710
R_free r_free	0.2240

fit	/app/data/saxs_computation/c7/1c7s/1c7s.fit
pddf	/app/data/pr_computation/c7/1c7s/1c7s.pr.out
profile	/app/data/saxs_computation/c7/1c7s/1c7s.dat

BETA-N-ACETYLHEXOSAMINIDASE MUTANT D539A COMPLEXED WITH DI-N-ACETYL-BETA-D-GLUCOSAMINE (CHITOBIASE)

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

BETA-N-ACETYLHEXOSAMINIDASE

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