SAXSdb — 3krg

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

Pectate lyase

Bacillus subtilis

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 22–420	Mutation：D173A,N180A,K247A	;alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid ; × 1 CO COBALT (II) ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, 50% PEG, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.196

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 3KRG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BN8 BACILLUS SUBTILIS PECTATE LYASE Deposited 1998-07-31	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 22–420（399 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；TYPE II CRYSTALS: 35 - 45 % 2-METHYL-2,4-PENTANDIOL 50 MM MOPS / 50 MM ETHANOLAMINE PH IN THE RANGE 6.50 TO 8.75	Resolution 1.80 Å
2BSP BACILLUS SUBTILIS PECTATE LYASE R279K MUTANT Deposited 1998-07-31	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 1–420（420 aa）	Mutation：R279K	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；30 % PEG 4000 0.2 M AMMONIUM SULPHATE 0.1 M SODIUM ACETATE AT PH 4.6	Resolution 1.80 Å R-free 0.225
2NZM Hexasaccharide I bound to Bacillus subtilis pectate lyase Deposited 2006-11-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–420（399 aa）	Mutation：R279A	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium citrate, 0.2M Ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.185
2O04 Pectate lyase bound to hexasaccharide compound II Deposited 2006-11-27	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–420（399 aa）	Mutation：R279A	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate pH 4.6, 0.2M Ammonium acetate, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.201
2O0V Pectate lyase bound to hexasaccharide compound III Deposited 2006-11-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–420（399 aa）	Mutation：R279A	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate pH 4.6, 0.2M Ammonium acetate, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.199
2O0W Pectate lyase bound to hexasaccharide compound IV Deposited 2006-11-28	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 22–420（399 aa）	Mutation：R279A	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate pH 4.6, 0.2M Ammonium acetate, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.198
2O17 Pectate lyase bound to hexasaccharide Deposited 2006-11-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–420（399 aa）	Mutation：R279A	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate pH 4.6, 0.2M Ammonium acetate, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.223
2O1D Pectate lyase bound to trisaccharide Deposited 2006-11-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–420（399 aa）	Mutation：R279A	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate pH 4.6, 0.2M Ammonium acetate, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.199
5AMV Structural insights into the loss of catalytic competence in pectate lyase at low pH Deposited 2015-09-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–420（399 aa）	Not recorded	CA CALCIUM ION × 1 ACT ACETATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；19% PEG 4K, 0.1M SODIUM ACETATE PH4, 0.2M AMMONIUM ACETATE	Resolution 1.57 Å R-free 0.193
5X2I Polygalacturonate Lyase by Fusing with a Self-assembling Amphipathic Peptide Deposited 2017-01-31	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 22–420（399 aa） Fragment：UNP residues 22-420	Not recorded	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.5；293 K；0.2 M sodium bromide, 20 mM Glycine-NaOH, 20 % polyethylene glycol 3350, 7 mM calcium chloride, 20 % glycerol	Resolution 2.05 Å R-free 0.200

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

View Construct and Data Evidence

UniProt name	PEL_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–399； UniProt 22–420

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	3krg
Deposition date deposition_date	2009-11-18
Structure title title	Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase
Keywords keywords	Michaelis complex, hexasaccharide, pectate lyase, lyase, Calcium, Secreted; LYASE
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	21.47 Å
Radius of gyration Rg (electron density) rg_electron	20.64 Å
Forward intensity I(0) i0	36781000.00
Molecular weight molecular_weight	44467.0 kDa
Excluded volume excluded_volume	54495 Å³
Envelope volume envelope_volume	61488 Å³
Hydration-shell volume shell_volume	24408 Å³
Envelope diameter envelope_diameter	68.6 Å
Shell Rg shell_rg	27.81 Å
Envelope Rg envelope_rg	20.89 Å
Shape Rg shape_rg	20.62 Å
Total Rg total_rg	21.49 Å
Total atoms total_atoms	3135
Residues n_residues	399
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	66.6 Å
Rg (real space) rg_real	21.35 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	3.6780e+07
I(0) uncertainty (real space) i0_real_error	4.4750e+05
Rg (reciprocal space) rg_reciprocal	21.38 Å
I(0) (reciprocal space) i0_reciprocal	36780000.0000
Solution quality estimate total_estimate	0.9032
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.4 Å
Skewness Skewness skewness	0.204
Kurtosis Kurtosis kurtosis	-0.431
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6576000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Pectate lyase
Molecular weight formula_weight	43300.1 kDa
EC 编号 ec_number	4.2.2.2
Mutation mutation	D173A,N180A,K247A
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	3858

ADLGHQTLGSNDGWGAYSTGTTGGSKASSSNVYTVSNRNQLVSALGKETNTTPKIIYIKGTIDMNVDDNLKPLGLNDYKDPEYDLDKYLKAYDPSTWGKKEPSGTQEEARARSQKNQKARVMVDIPANTTIVGSGTNAKVVGGNFQIKSDNVIIRNIEFQDAYDYFPQWDPTAGSSGNWASQYDNITINGGTHIWIDHCTFNDGSRPDSTSPKYYGRKYQHHDGQTDASNGANYITMSYNYYHDHDASSIFGSSDSKTSDDGKLKITLHHNRYKNIVQRAPRVRFGQVHVYNNYYEGSTSSSSYPFSYAWGIGKSSKIYAQNNVIDVPGLSAAKTISVFSGGTALYDSGTLLNGTQINASAANGLSSSVGWTPSLHGSIDASANVKSNVINQAGAGKLN

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	;alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid ;
Molecular weight formula_weight	1074.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	723

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3krga_
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.1 — Pectin lyase-like
Family Family family	b.80.1.1 — Pectate lyase-like

CATH v4.4 (1 domains)

Domain ID domain_id	3krgA00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	10 — Single-stranded right-handed beta-helix, Pectin lyase-like

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8. Citations (1)

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Unit-cell length a length_a	50.626 Å
Unit-cell length b length_b	69.066 Å
Unit-cell length c length_c	59.656 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.85 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	29.180 Å
R factor r_factor	0.1350
R_work r_work	0.1320
R_free r_free	0.1960

fit	/app/data/saxs_computation/kr/3krg/3krg.fit
pddf	/app/data/pr_computation/kr/3krg/3krg.pr.out
profile	/app/data/saxs_computation/kr/3krg/3krg.dat

Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase

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

Pectate 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