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1e3c

Crystal structure of an Arylsulfatase A mutant C69S soaked in synthetic substrate

Method: X-RAY DIFFRACTION Dmax: 73.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Arylsulfatase A

Homo sapiens

UniProt P15289

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 P； UniProt 19–507 Mutation：C69S 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；291 K；PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION IN HANGING DROPS AT 291 K. SOLUTION CONTAINING 10MG/ML PROTEIN, 10 MM TRIS/HCL (PH 7.4) AND 150 MM NACL WAS MIXED WITH SAME VOLUME OF RESERVOIR SOLUTION, CONTAINING 100 MM NA-ACETATE (PH 5.0 - 5.4) AND 10 - 13 % PEG 6000 Resolution 2.65 Å R-free 0.243

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 1E3C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AUK HUMAN ARYLSULFATASE A Deposited 1997-08-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 19–507（489 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；291 K；PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION IN HANGING DROPS AT 291 K. SOLUTION CONTAINING 10MG/ML PROTEIN, 10 MM TRIS/HCL (PH 7.4) AND 150 MM NACL WAS MIXED WITH SAME VOLUME OF RESERVOIR SOLUTION, CONTAINING 100 MM NA-ACETATE (PH 5.0 - 5.4) AND 10 - 13 % PEG 6000, vapor diffusion - hanging drop
Resolution 2.10 Å R-free 0.273
1E1Z Crystal structure of an Arylsulfatase A mutant C69S Deposited 2000-05-12 Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain P 19–507（489 aa）
Mutation：C69S MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；291 K；PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION IN HANGING DROPS AT 291 K. SOLUTION CONTAINING 10MG/ML PROTEIN, 10 MM TRIS/HCL (PH 7.4) AND 150 MM NACL WAS MIXED WITH SAME VOLUME OF RESERVOIR SOLUTION, CONTAINING 100 MM NA-ACETATE (PH 5.0 - 5.4) AND 10 - 13 % PEG 6000
Resolution 2.40 Å R-free 0.243
1E2S Crystal structure of an Arylsulfatase A mutant C69A Deposited 2000-05-24 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain P 19–507（489 aa）
Mutation：C69A MG MAGNESIUM ION × 2 CSN N,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；291 K；PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION IN HANGING DROPS AT 291 K. SOLUTION CONTAINING 10MG/ML PROTEIN, 10 MM TRIS/HCL (PH 7.4) AND 150 MM NACL WAS MIXED WITH SAME VOLUME OF RESERVOIR SOLUTION, CONTAINING 100 MM NA-ACETATE (PH 5.0 - 5.4) AND 10 - 13 % PEG 6000
Resolution 2.35 Å R-free 0.236
1E33 Crystal structure of an Arylsulfatase A mutant P426L Deposited 2000-06-06 Different mutation/modification Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain P 19–507（489 aa）
Mutation：P426L Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；291 K；PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION IN HANGING DROPS AT 291 K. SOLUTION CONTAINING 10MG/ML PROTEIN, 10 MM TRIS/HCL (PH 7.4) AND 150 MM NACL WAS MIXED WITH SAME VOLUME OF RESERVOIR SOLUTION, CONTAINING 100 MM NA-ACETATE (PH 5.0 - 5.4) AND 10 - 13 % PEG 6000
Resolution 2.50 Å R-free 0.250
1N2K Crystal structure of a covalent intermediate of endogenous human arylsulfatase A Deposited 2002-10-23 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 19–507（489 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；cacodylate, sodium fluoride, PEG8000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.75 Å R-free 0.239
1N2L Crystal structure of a covalent intermediate of endogenous human arylsulfatase A Deposited 2002-10-23 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 19–507（489 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；cacodylate, sodium fluoride, PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.223
2AIJ Formylglycine generating enzyme C336S mutant covalently bound to substrate peptide CTPSR Deposited 2005-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 69–73（5 aa）
Not recorded CA CALCIUM ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, Calcium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.55 Å R-free 0.178
2AIK Formylglycine generating enzyme C336S mutant covalently bound to substrate peptide LCTPSRA Deposited 2005-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 68–74（7 aa）
Not recorded CA CALCIUM ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, Calcium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.73 Å R-free 0.174

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ARSA_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain P； PDBConstruct 1–489； UniProt 19–507

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 1e3c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1e3c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1e3c
Deposition date deposition_date2000-06-13
Structure title titleCrystal structure of an Arylsulfatase A mutant C69S soaked in synthetic substrate
Keywords keywordsHYDROLASE, CEREBROSIDE-3-SULFATE HYDROLYSIS, LYSOSOMAL ENZYME, FORMYLGLYCINE; HYDROLASE
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_guinier22.38 Å
Radius of gyration Rg (electron density) rg_electron21.30 Å
Forward intensity I(0) i043662100.00
Molecular weight molecular_weight51302.0 kDa
Excluded volume excluded_volume64074 ų
Envelope volume envelope_volume71491 ų
Hydration-shell volume shell_volume27128 ų
Envelope diameter envelope_diameter77.0 Å
Shell Rg shell_rg28.99 Å
Envelope Rg envelope_rg21.56 Å
Shape Rg shape_rg21.28 Å
Total Rg total_rg22.24 Å
Total atoms total_atoms3611
Residues n_residues481
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 dmax73.3 Å
Rg (real space) rg_real22.25 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real4.3660e+07
I(0) uncertainty (real space) i0_real_error5.5880e+05
Rg (reciprocal space) rg_reciprocal22.28 Å
I(0) (reciprocal space) i0_reciprocal43660000.0000
Solution quality estimate total_estimate0.8809
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.9 Å
Skewness Skewness skewness0.147
Kurtosis Kurtosis kurtosis-0.378
Angular range angular_range— – 0.3550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9956000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1e3cp_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.76 — Alkaline phosphatase-like
Superfamily Superfamily superfamilyc.76.1 — Alkaline phosphatase-like
Family Family familyc.76.1.2 — Arylsulfatase

CATH v4.4 (2 domains)

Domain ID domain_id1e3cP01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology720 — Alkaline Phosphatase, subunit A
Homologous superfamily homologous superfamily10 — Alkaline Phosphatase, subunit A
Domain ID domain_id1e3cP02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)