SAXSdb — 2wdb

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

HYALURONOGLUCOSAMINIDASE

CLOSTRIDIUM PERFRINGENS

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 807–975	Fragment：RESIDUES 807-975	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.03 Å R-free 0.260
2	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 807–975	Fragment：RESIDUES 807-975	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.03 Å R-free 0.260
3	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 807–975	Fragment：RESIDUES 807-975	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.03 Å R-free 0.260
4	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 807–975	Fragment：RESIDUES 807-975	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.03 Å R-free 0.260

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 2WDB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JNK Solution structure of a dockerin-containing modular pair from a family 84 glycoside hydrolase Deposited 2007-01-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1498–1628（131 aa） Fragment：sequence database residues 1498-1628	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Pressure ambient NMR sample composition 1mM protein, 25 mM HEPES, 50 mM sodium chloride, 5 mM Calclium chloride, 0.5 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2OZN The Cohesin-Dockerin Complex of NagJ and NagH from Clostridium perfringens Deposited 2007-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1498–1628（131 aa） Fragment：Fivar-Dockerin modular pair (residues 1498-1628)	Not recorded	CL CHLORIDE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；21% (w/v) polyethylene glycol 2000, 0.2M ammonium sulfate, 100mM sodium acetate, pH 4.5	Resolution 1.60 Å R-free 0.246
2W1Q Unique ligand binding specificity for a family 32 Carbohydrate- Binding Module from the Mu toxin produced by Clostridium perfringens Deposited 2008-10-20	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 807–975（169 aa） Fragment：CARBOHYDRATE BINDING MODULE, RESIDUES 807-975	Not recorded	CA CALCIUM ION × 1 NA SODIUM ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å R-free 0.199
2W1Q Unique ligand binding specificity for a family 32 Carbohydrate- Binding Module from the Mu toxin produced by Clostridium perfringens Deposited 2008-10-20	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 807–975（169 aa） Fragment：CARBOHYDRATE BINDING MODULE, RESIDUES 807-975	Not recorded	CA CALCIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å R-free 0.199
2W1S Unique ligand binding specificity of a family 32 Carbohydrate-Binding Module from the Mu toxin produced by Clostridium perfringens Deposited 2008-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 807–975（169 aa） Fragment：FAMILY 32 CBM, RESIDUES 807-975	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 NA SODIUM ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.45 Å R-free 0.226
2W1S Unique ligand binding specificity of a family 32 Carbohydrate-Binding Module from the Mu toxin produced by Clostridium perfringens Deposited 2008-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 807–975（169 aa） Fragment：FAMILY 32 CBM, RESIDUES 807-975	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.45 Å R-free 0.226
2W1U A family 32 carbohydrate-binding module, from the Mu toxin produced by Clostridium perfringens, in complex with beta-D-glcNAc-beta(1,3) galNAc Deposited 2008-10-20	Different construct Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 807–975（169 aa） Fragment：FAMILY 32 CBM, RESIDUES 807-975	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.213
2W1U A family 32 carbohydrate-binding module, from the Mu toxin produced by Clostridium perfringens, in complex with beta-D-glcNAc-beta(1,3) galNAc Deposited 2008-10-20	Different construct Different ligand/ion Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 807–975（169 aa） Fragment：FAMILY 32 CBM, RESIDUES 807-975	Not recorded	CA CALCIUM ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.213
2W1U A family 32 carbohydrate-binding module, from the Mu toxin produced by Clostridium perfringens, in complex with beta-D-glcNAc-beta(1,3) galNAc Deposited 2008-10-20	Different construct Different ligand/ion Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain C 807–975（169 aa） Fragment：FAMILY 32 CBM, RESIDUES 807-975	Not recorded	CA CALCIUM ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.213
2W1U A family 32 carbohydrate-binding module, from the Mu toxin produced by Clostridium perfringens, in complex with beta-D-glcNAc-beta(1,3) galNAc Deposited 2008-10-20	Different construct Different ligand/ion Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain D 807–975（169 aa） Fragment：FAMILY 32 CBM, RESIDUES 807-975	Not recorded	CA CALCIUM ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.213

5 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NAGH_CLOPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–192； UniProt 807–975 Author chain B； PDBConstruct 24–192； UniProt 807–975 Author chain C； PDBConstruct 24–192； UniProt 807–975 Author chain D； PDBConstruct 24–192； UniProt 807–975

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	2wdb
Deposition date deposition_date	2009-03-23
Structure title title	A family 32 carbohydrate-binding module, from the Mu toxin produced by Clostridium perfringens, in complex with beta-D-glcNAc-beta(1,2) mannose
Keywords keywords	;FAMILY 32 CARBOHYDRATE BINDING MODULE, FAMILY 84 GLYCOSIDE HYDROLASE, GLYCOSIDASE, HEXOSAMINIDASE, CLOSTRIDIUM PERFRINGENS, CBM, TOXIN, SECRETED, VIRULENCE, 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	25.63 Å
Radius of gyration Rg (electron density) rg_electron	24.69 Å
Forward intensity I(0) i0	70028600.00
Molecular weight molecular_weight	65286.0 kDa
Excluded volume excluded_volume	81533 Å³
Envelope volume envelope_volume	98243 Å³
Hydration-shell volume shell_volume	32428 Å³
Envelope diameter envelope_diameter	80.9 Å
Shell Rg shell_rg	32.44 Å
Envelope Rg envelope_rg	24.60 Å
Shape Rg shape_rg	24.65 Å
Total Rg total_rg	25.64 Å
Total atoms total_atoms	4606
Residues n_residues	569
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	78.3 Å
Rg (real space) rg_real	25.47 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	7.0030e+07
I(0) uncertainty (real space) i0_real_error	9.6760e+05
Rg (reciprocal space) rg_reciprocal	25.52 Å
I(0) (reciprocal space) i0_reciprocal	70030000.0000
Solution quality estimate total_estimate	0.9046
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.8 Å
Skewness Skewness skewness	0.109
Kurtosis Kurtosis kurtosis	-0.488
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12150000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.982

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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	HYALURONOGLUCOSAMINIDASE
Molecular weight formula_weight	21395.6 kDa
EC 编号 ec_number	3.2.1.35
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5090

MGSSHHHHHHSSGLVPRGSHMASNPSLIRSESWQVYEGNEANLLDGDDNTGVWYKTLNGDTSLAGEFIGLDLGKEIKLDGIRFVIGKNGGGSSDKWNKFKLEYSLDNESWTTIKEYDKTGAPAGKDVIEESFETPISAKYIRLTNMENINKWLTFSEFAIVSDELENAGNKENVYTNTELDLLSLAKEDVTK

来源 Source

来源生物 organism	CLOSTRIDIUM PERFRINGENS
NCBI Class编号 ncbi_taxonomy_id	1502
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose
Molecular weight formula_weight	383.3 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 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	476

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2wdbA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2wdbB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2wdbC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2wdbD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

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8. Citations (1)

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Unit-cell length a length_a	91.276 Å
Unit-cell length b length_b	91.276 Å
Unit-cell length c length_c	132.701 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.030 Å
Low-resolution limit resolution_low	79.060 Å
R factor r_factor	0.1974
R_work r_work	0.1941
R_free r_free	0.2596

fit	/app/data/saxs_computation/wd/2wdb/2wdb.fit
pddf	/app/data/pr_computation/wd/2wdb/2wdb.pr.out
profile	/app/data/saxs_computation/wd/2wdb/2wdb.dat

A family 32 carbohydrate-binding module, from the Mu toxin produced by Clostridium perfringens, in complex with beta-D-glcNAc-beta(1,2) mannose

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

HYALURONOGLUCOSAMINIDASE

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