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5amv

Structural insights into the loss of catalytic competence in pectate lyase at low pH

Method: X-RAY DIFFRACTION Dmax: 66.1 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PECTATE LYASE

BACILLUS SUBTILIS

UniProt P39116

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 Not recorded alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid × 1 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

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 5AMV 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 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
3KRG Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase Deposited 2009-11-18 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：D173A,N180A,K247A 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
5X2I Polygalacturonate Lyase by Fusing with a Self-assembling Amphipathic Peptide Deposited 2017-01-31 Different construct 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 PLY_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.

SAXS scattering curve SAXS Profile

SAXS profile for 5amv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5amv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5amv
Deposition date deposition_date2015-09-02
Structure title titleStructural insights into the loss of catalytic competence in pectate lyase at low pH
Keywords keywordsLYASE, PECTATE LYASE, BACILLUS SUBTILLIS, CATALYTIC ACTIVITY; LYASE
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_guinier21.53 Å
Radius of gyration Rg (electron density) rg_electron20.62 Å
Forward intensity I(0) i036126300.00
Molecular weight molecular_weight44008.0 kDa
Excluded volume excluded_volume53973 ų
Envelope volume envelope_volume61118 ų
Hydration-shell volume shell_volume24222 ų
Envelope diameter envelope_diameter68.2 Å
Shell Rg shell_rg27.82 Å
Envelope Rg envelope_rg20.86 Å
Shape Rg shape_rg20.61 Å
Total Rg total_rg21.50 Å
Total atoms total_atoms3105
Residues n_residues399
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 dmax66.1 Å
Rg (real space) rg_real21.40 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real3.6130e+07
I(0) uncertainty (real space) i0_real_error4.2540e+05
Rg (reciprocal space) rg_reciprocal21.43 Å
I(0) (reciprocal space) i0_reciprocal36130000.0000
Solution quality estimate total_estimate0.9066
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.3 Å
Skewness Skewness skewness0.185
Kurtosis Kurtosis kurtosis-0.459
Angular range angular_range— – 0.3700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6223000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5amva_
Class classb — All beta proteins
Fold Fold foldb.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamilyb.80.1 — Pectin lyase-like
Family Family familyb.80.1.1 — Pectate lyase-like

CATH v4.4 (1 domains)

Domain ID domain_id5amvA00
Class class2 — Mainly Beta
Architecture architecture160 — 3 Solenoid
Topology topology20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily10 — Single-stranded right-handed beta-helix, Pectin lyase-like
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8. Citations (1)

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9. Files and Curves (10)