← Back to search
1e5n

E246C mutant of P fluorescens subsp. cellulosa xylanase A in complex with xylopentaose

Method: X-RAY DIFFRACTION Dmax: 79.2 Å Quality: EXCELLENT
▼

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

ENDO-1,4-BETA-XYLANASE A

PSEUDOMONAS FLUORESCENS

UniProt P14768

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 264–611 Fragment：CATALYTIC DOMAIN RESIDUES 264-611 Mutation：YES beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；HANGING DROP (10 MG/ML OF PROTEIN) WITH A RESERVOIR OF 0.1 M SODIUM CACODYLATE PH 6.5, 200 MM CALCIUM ACETATE, 1 MM BETA-MERCAPTOETHANOL, 14-18% PEG 8000 Resolution 3.20 Å R-free 0.245
2 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 264–611 Fragment：CATALYTIC DOMAIN RESIDUES 264-611 Mutation：YES beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；HANGING DROP (10 MG/ML OF PROTEIN) WITH A RESERVOIR OF 0.1 M SODIUM CACODYLATE PH 6.5, 200 MM CALCIUM ACETATE, 1 MM BETA-MERCAPTOETHANOL, 14-18% PEG 8000 Resolution 3.20 Å R-free 0.245

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 1E5N Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CLX CATALYTIC CORE OF XYLANASE A Deposited 1995-08-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 265–611（347 aa） Fragment：CATALYTIC CORE, RESIDUES 264 - 611
Chain B 265–611（347 aa） Fragment：CATALYTIC CORE, RESIDUES 264 - 611
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 1.80 Å
1CLX CATALYTIC CORE OF XYLANASE A Deposited 1995-08-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 265–611（347 aa） Fragment：CATALYTIC CORE, RESIDUES 264 - 611
Chain D 265–611（347 aa） Fragment：CATALYTIC CORE, RESIDUES 264 - 611
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 1.80 Å
1E8R SOLUTION STRUCTURE OF TYPE X CBD Deposited 2000-09-28 Different construct Different mutation/modification 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 179–228（50 aa） Fragment：TYPE X CELLULOSE BINDING DOMAIN (CBDX)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；323 K；Ionic strength (raw mmCIF value) 100MM NACL；Pressure AMBIENT
NMR sample composition 1MM CBDX
NMR sample composition 50MM SODIUM PHOSPHATE BUFFER
NMR sample composition 100MM SODIUM CHLORIDE
Resolution not provided
1QLD Solution structure of type X CBM Deposited 1999-08-26 Different construct Different mutation/modification 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 180–228（49 aa） Fragment：CELLULOSE BINDING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；323 K；Ionic strength (raw mmCIF value) 100 MM NACL；Pressure AMBIENT
NMR sample composition 90% WATER / 10% D2O
Resolution not provided
1W2P The 3-dimensional structure of a xylanase (Xyn10A) from Cellvibrio japonicus Deposited 2004-07-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 265–609（345 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 265-611
Chain A 610–611（2 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 265-611
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.45 Å R-free 0.152
1W2P The 3-dimensional structure of a xylanase (Xyn10A) from Cellvibrio japonicus Deposited 2004-07-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 265–609（345 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 265-611
Chain B 610–611（2 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 265-611
Not recorded CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.45 Å R-free 0.152
1W2V The 3-dimensional structure of a thermostable mutant of a xylanase (Xyn10A) from Cellvibrio japonicus Deposited 2004-07-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 265–611（347 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 265-611
Mutation：YES CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.55 Å R-free 0.186
1W2V The 3-dimensional structure of a thermostable mutant of a xylanase (Xyn10A) from Cellvibrio japonicus Deposited 2004-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 265–611（347 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 265-611
Mutation：YES CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.55 Å R-free 0.186
1W32 The 3-dimensional structure of a thermostable mutant of a xylanase (Xyn10A) from Cellvibrio japonicus Deposited 2004-07-12 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 265–611（347 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 265-611
Mutation：YES CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.20 Å R-free 0.144
1W32 The 3-dimensional structure of a thermostable mutant of a xylanase (Xyn10A) from Cellvibrio japonicus Deposited 2004-07-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 265–611（347 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 265-611
Mutation：YES CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.20 Å R-free 0.144
1W3H The 3-dimensional structure of a thermostable mutant of a xylanase (Xyn10A) from Cellvibrio japonicus Deposited 2004-07-15 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 265–611（347 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 265-611
Mutation：YES CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å R-free 0.251
1W3H The 3-dimensional structure of a thermostable mutant of a xylanase (Xyn10A) from Cellvibrio japonicus Deposited 2004-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 265–611（347 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 265-611
Mutation：YES CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å R-free 0.251
1XYS CATALYTIC CORE OF XYLANASE A E246C MUTANT Deposited 1994-09-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 265–611（347 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1XYS CATALYTIC CORE OF XYLANASE A E246C MUTANT Deposited 1994-09-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 265–611（347 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å

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

View Construct and Data Evidence
UniProt name XYNA_PSEFL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–348； UniProt 264–611 Author chain B； PDBConstruct 1–348； UniProt 264–611

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 1e5n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1e5n
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1e5n
Deposition date deposition_date2000-07-27
Structure title titleE246C mutant of P fluorescens subsp. cellulosa xylanase A in complex with xylopentaose
Keywords keywordsGLYCOSYL HYDROLASE, FAMILY 10, XYLAN DEGRADATION, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier26.62 Å
Radius of gyration Rg (electron density) rg_electron25.73 Å
Forward intensity I(0) i0104958000.00
Molecular weight molecular_weight77880.0 kDa
Excluded volume excluded_volume96147 ų
Envelope volume envelope_volume112780 ų
Hydration-shell volume shell_volume35548 ų
Envelope diameter envelope_diameter80.1 Å
Shell Rg shell_rg34.12 Å
Envelope Rg envelope_rg25.45 Å
Shape Rg shape_rg25.72 Å
Total Rg total_rg26.58 Å
Total atoms total_atoms5494
Residues n_residues692
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
▼

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

Maximum dimension Dmax dmax79.2 Å
Rg (real space) rg_real26.48 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real1.0500e+08
I(0) uncertainty (real space) i0_real_error1.3270e+06
Rg (reciprocal space) rg_reciprocal26.53 Å
I(0) (reciprocal space) i0_reciprocal105000000.0000
Solution quality estimate total_estimate0.9085
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary77.9 Å
Skewness Skewness skewness0.198
Kurtosis Kurtosis kurtosis-0.494
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41510000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.956; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.955
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1e5na_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.3 — beta-glycanases
Domain ID domain_idd1e5nb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.3 — beta-glycanases

CATH v4.4 (2 domains)

Domain ID domain_id1e5nA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1e5nB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
▶

8. Citations (4)

▶

9. Files and Curves (10)