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1xys

CATALYTIC CORE OF XYLANASE A E246C MUTANT

Method: X-RAY DIFFRACTION Dmax: 79.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

XYLANASE A

Cellvibrio japonicus

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 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 265–611 Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.50 Å
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 265–611 Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.50 Å

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 1XYS 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
1E5N E246C mutant of P fluorescens subsp. cellulosa xylanase A in complex with xylopentaose Deposited 2000-07-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 264–611（348 aa） Fragment：CATALYTIC DOMAIN RESIDUES 264-611
Mutation：YES 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
1E5N E246C mutant of P fluorescens subsp. cellulosa xylanase A in complex with xylopentaose Deposited 2000-07-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 264–611（348 aa） Fragment：CATALYTIC DOMAIN RESIDUES 264-611
Mutation：YES 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
1E8R SOLUTION STRUCTURE OF TYPE X CBD Deposited 2000-09-28 Different construct 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 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 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 ligand/ion 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 mutation/modification 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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

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 1–347； UniProt 265–611 Author chain B； PDBConstruct 1–347； UniProt 265–611

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 1xys

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1xys
Deposition date deposition_date1994-09-02
Structure title titleCATALYTIC CORE OF XYLANASE A E246C MUTANT
Keywords keywordsFAMILY F XYLANASE, FAMILY 10 OF GLYCOSYL-HYDROLASE, HYDROLASE; 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_guinier26.45 Å
Radius of gyration Rg (electron density) rg_electron25.88 Å
Forward intensity I(0) i098061600.00
Molecular weight molecular_weight76418.0 kDa
Excluded volume excluded_volume92505 ų
Envelope volume envelope_volume76914 ų
Hydration-shell volume shell_volume26518 ų
Envelope diameter envelope_diameter77.1 Å
Shell Rg shell_rg31.12 Å
Envelope Rg envelope_rg23.83 Å
Shape Rg shape_rg26.05 Å
Total Rg total_rg26.27 Å
Total atoms total_atoms2
Residues n_residues—
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 dmax79.3 Å
Rg (real space) rg_real26.30 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real9.8060e+07
I(0) uncertainty (real space) i0_real_error1.1690e+06
Rg (reciprocal space) rg_reciprocal26.35 Å
I(0) (reciprocal space) i0_reciprocal98060000.0000
Solution quality estimate total_estimate0.9101
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.1 Å
Skewness Skewness skewness0.160
Kurtosis Kurtosis kurtosis-0.520
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha25210000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.957
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1xysa_
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_idd1xysb_
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
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8. Citations (3)

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9. Files and Curves (10)