SAXSdb — 1w3y

▼

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

HYALURONATE LYASE

STREPTOCOCCUS PNEUMONIAE

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 297–1021	Not recorded	PVC (2E,4R,5S)-2,3,4,5-TETRAHYDROXY-6-(PALMITOYLOXY)HEX-2-ENOIC ACID × 1 XYL Xylitol × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；62% SATURATED AMMONIUM SULFATE, 100 MM SODIUM CACODYLATE PH6.00, 100 MM SODIUM CHLORIDE, 10 MM EDTA, 2% DIOXANE	Resolution 1.65 Å R-free 0.210

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 1W3Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C82 MECHANISM OF HYALURONAN BINDING AND DEGRADATION: STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN COMPLEX WITH HYALURONIC ACID DISACCHARIDE AT 1.7 A RESOLUTION Deposited 2000-04-05	Different construct 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 168–892（725 aa）	Not recorded	CAC CACODYLATE ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；293 K；AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.0, EVAPORATION, temperature 293K	Resolution 1.70 Å R-free 0.257
1EGU CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE AT 1.56 A RESOLUTION Deposited 2000-02-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 168–898（731 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；62% Saturated Ammonium Sulfate, 100 mM Sodium Cacodylate pH6.00, 100 mM Sodium Chloride, 10 mM EDTA, 2% dioxane , VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 1.56 Å R-free 0.236
1F9G CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE COCRYSTALLIZED WITH ASCORBIC ACID Deposited 2000-07-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 168–892（725 aa）	Not recorded	ASC ASCORBIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；ammonium sulfate, sodium cacodylate, dioxane, sodium chloride, ascorbic acid , pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.252
1N7N Streptococcus pneumoniae Hyaluronate Lyase W292A Mutant Deposited 2002-11-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 170–890（721 aa）	Mutation：W292A mutant	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.209
1N7O Streptococcus pneumoniae Hyaluronate Lyase F343V Mutant Deposited 2002-11-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 170–890（721 aa）	Mutation：F343V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；AMMONIUM SULFATE, SODIUM CACODYLATE , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.50 Å R-free 0.211
1N7P Streptococcus pneumoniae Hyaluronate Lyase W292A/F343V Double Mutant Deposited 2002-11-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 170–890（721 aa）	Mutation：W292A/F343V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.55 Å R-free 0.234
1OJM SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX WITH UNSULPHATED CHONDROITIN DISACCHARIDE Deposited 2003-07-11	Different construct 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 291–1009（719 aa） Fragment：HYALURONATE LYASE, RESIDUES 287-1009	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；3.5M AMMONIUM SULFATE, 200MM SODIUM CACODYLATE, PH 6.0	Resolution 1.78 Å R-free 0.224
1OJN SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX OF THE TYR408PHE MUTANT WITH 6-SULPHATED CHONDROITIN DISACCHARIDE Deposited 2003-07-11	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 285–1009（725 aa） Fragment：HYALURONATE LYASE, RESIDUES 285-1009	Mutation：YES	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；3.5M AMMONIUM SULFATE, 200MM SODIUM CACODYLATE, PH 6.0	Resolution 1.60 Å R-free 0.209
1OJO SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX OF THE TYR408PHE MUTANT WITH 4-SULPHATED CHONDROITIN DISACCHARIDE Deposited 2003-07-11	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 285–1009（725 aa） Fragment：HYALURONATE LYASE, RESIDUES 285-1009	Mutation：YES	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；3.5M AMMONIUM SULFATE, 200MM SODIUM CACODYLATE, PH 6.0	Resolution 1.75 Å R-free 0.219
1OJP SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX WITH 6-SULPHATED CHONDROITIN DISACCHARIDE Deposited 2003-07-11	Different construct 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 285–1009（725 aa） Fragment：HYALURONATE LYASE, RESIDUES 285-1009	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；3.5M AMMONIUM SULFATE, 200MM SODIUM CACODYLATE, PH 6.0	Resolution 1.90 Å R-free 0.221
2BRP Crystal structure of S. pneumoniae hyaluronate lyase in complex with W249b Deposited 2005-05-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 285–1009（725 aa）	Not recorded	SIE SULFAMIC ACID 1-DECYL-2-(4-SULFAMOYLOXYPHENYL)-1H-INDOL-6-YL ESTER × 1 XLS D-xylose × 3 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.00	Resolution 2.00 Å R-free 0.202
2BRV Crystal structure of Streptococcus Pneumoniae Hyaluronate Lyase from 70percent saturated malonate. Deposited 2005-05-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 285–1009（725 aa）	Not recorded	MLA MALONIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；pH 7.60	Resolution 3.30 Å R-free 0.327
2BRW Crystal structure of Streptococcus Pneumoniae Hyaluronate Lyase from 30percent PEGMME. Deposited 2005-05-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 285–1009（725 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；30% POLYETHYLENE GLYCOL MONOMETHYL ETHER (PEGMME) 2000, 0.1 M MES BUFFER, PH 6.5	Resolution 2.80 Å R-free 0.277
2BRW Crystal structure of Streptococcus Pneumoniae Hyaluronate Lyase from 30percent PEGMME. Deposited 2005-05-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 285–1009（725 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；30% POLYETHYLENE GLYCOL MONOMETHYL ETHER (PEGMME) 2000, 0.1 M MES BUFFER, PH 6.5	Resolution 2.80 Å R-free 0.277
4D0Q Hyaluronan Binding Module of the Streptococcal Pneumoniae Hyaluronate Lyase Deposited 2014-04-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 54–212（159 aa） Fragment：HYALURONAN BINDING DOMAIN, RESIDUES 54-212	Not recorded	EDO 1,2-ETHANEDIOL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；292 K；BY THE SITTING DROP VAPOUR DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF THE PROTEIN SOLUTION WITH A MOTHER LIQUOR CONSISTING OF 18% (W/V) POLYETHYLENE GLYCOL 3,350 AND 0.1 M SODIUM ACETATE (PH 5.5) AT 292 K.	Resolution 1.20 Å R-free 0.159

14 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HYSA_STRPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–725； UniProt 297–1021

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1w3y
Deposition date deposition_date	2004-07-21
Structure title title	Crystal structure of S. pneumoniae hyaluronate lyase in complex with palmitoyl-vitamin C
Keywords keywords	(ALFA5/ALFA5) BARREL, LYASE, PEPTIDOGLYCAN-ANCHOR; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.37 Å
Radius of gyration Rg (electron density) rg_electron	27.55 Å
Forward intensity I(0) i0	116119000.00
Molecular weight molecular_weight	83363.0 kDa
Excluded volume excluded_volume	103490 Å³
Envelope volume envelope_volume	122650 Å³
Hydration-shell volume shell_volume	36733 Å³
Envelope diameter envelope_diameter	95.7 Å
Shell Rg shell_rg	35.45 Å
Envelope Rg envelope_rg	27.66 Å
Shape Rg shape_rg	27.54 Å
Total Rg total_rg	28.33 Å
Total atoms total_atoms	5862
Residues n_residues	721
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	90.7 Å
Rg (real space) rg_real	28.35 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.1610e+08
I(0) uncertainty (real space) i0_real_error	1.5530e+06
Rg (reciprocal space) rg_reciprocal	28.36 Å
I(0) (reciprocal space) i0_reciprocal	116100000.0000
Solution quality estimate total_estimate	0.7172
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.4 Å
Skewness Skewness skewness	0.366
Kurtosis Kurtosis kurtosis	-0.342
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30950000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.999; Smooth: 0.956

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	HYALURONATE LYASE
Molecular weight formula_weight	83561.9 kDa
EC 编号 ec_number	4.2.2.1
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	6471

ASVKDTYTDRLDDWNGIIAGNQYYDSKNDQMAKLNQELEGKVADSLSSISSQADRIYLWEKFSNYKTSANLTATYRKLEEMAKQVTNPSSRYYQDETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEIGTPRAINNTLSLMKEYFSDEEIKKYTDVIEKFVPDPEHFRKTTDNPFKALGGNLVDMGRVKVIAGLLRKDDQEISSTIRSIEQVFKLVDQGEGFYQDGSYIDHTNVAYTGAYGNVLIDGLSQLLPVIQKTKNPIDKDKMQTMYHWIDKSFAPLLVNGELMDMSRGRSISRANSEGHVAAVEVLRGIHRIADMSEGETKQRLQSLVKTIVQSDSYYDVFKNLKTYKDISLMQSLLSDAGVASVPRTSYLSAFNKMDKTAMYNAEKGFGFGLSLFSSRTLNYEHMNKENKRGWYTSDGMFYLYNGDLSHYSDGYWPTVNPYKMPGTTETDAKRADSDTGKVLPSAFVGTSKLDDANATATMDFTNWNQTLTAHKSWFMLKDKIAFLGSNIQNTSTDTAATTIDQRKLESSNPYKVYVNDKEASLTEQEKDYPETQSVFLESSDSKKNIGYFFFKKSSISMSKALQKGAWKDINEGQSDKEVENEFLTISQAHKQNGDSYGYMLIPNVDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVYTIRKEGDEYKIAYYNPETQESAPDQEVFKKLEQHHHHHH

来源 Source

来源生物 organism	STREPTOCOCCUS PNEUMONIAE
NCBI Class编号 ncbi_taxonomy_id	1313
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	(2E,4R,5S)-2,3,4,5-TETRAHYDROXY-6-(PALMITOYLOXY)HEX-2-ENOIC ACID
Molecular weight formula_weight	432.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	Xylitol
Molecular weight formula_weight	152.1 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	564

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1w3ya1
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.3 — Chondroitin AC/alginate lyase
Family Family family	a.102.3.2 — Hyaluronate lyase-like catalytic, N-terminal domain

Domain ID domain_id	d1w3ya2
Class class	b — All beta proteins
Fold Fold fold	b.24 — Hyaluronate lyase-like, C-terminal domain
Superfamily Superfamily superfamily	b.24.1 — Hyaluronate lyase-like, C-terminal domain
Family Family family	b.24.1.1 — Hyaluronate lyase-like, C-terminal domain

Domain ID domain_id	d1w3ya3
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.2 — Hyaluronate lyase-like, central domain

CATH v4.4 (3 domains)

Domain ID domain_id	1w3yA01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1w3yA02
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	100 — Chondroitin AC/alginate lyase

Domain ID domain_id	1w3yA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	220 — Chondroitinase Ac; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Polysaccharide lyase family 8-like, C-terminal

▶

8. Citations (1)

▶

Unit-cell length a length_a	84.131 Å
Unit-cell length b length_b	102.714 Å
Unit-cell length c length_c	102.410 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	45.910 Å
R factor r_factor	0.1924
R_work r_work	0.1924
R_free r_free	0.2100

fit	/app/data/saxs_computation/w3/1w3y/1w3y.fit
pddf	/app/data/pr_computation/w3/1w3y/1w3y.pr.out
profile	/app/data/saxs_computation/w3/1w3y/1w3y.dat

Crystal structure of S. pneumoniae hyaluronate lyase in complex with palmitoyl-vitamin C

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

HYALURONATE LYASE

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