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1bg4

XYLANASE FROM PENICILLIUM SIMPLICISSIMUM

Method: X-RAY DIFFRACTION Dmax: 62.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ENDO-1,4-BETA-XYLANASE

OrganismNot specified

UniProt P56588

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 2–302 Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 6 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 GOL GLYCEROL × 7 X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.4；277 K；PROTEIN WAS CRYSTALLIZED FROM 1.9M (NH4)2SO4, 0.1M TRISHCL PH 8.4 AT 4 C, temperature 277K Resolution 1.75 Å R-free 0.229

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 1BG4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B31 XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, NATIVE WITH PEG200 AS CRYOPROTECTANT Deposited 1998-12-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–302（302 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.4；CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 1.9M (NH4)2SO4, 0.1M TRISHCL PH 8.4 AT 4 C
Resolution 1.75 Å R-free 0.243
1B3V XYLANASE FROM PENICILLIUM SIMPLICISSIMUM, COMPLEX WITH XYLOSE Deposited 1998-12-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–302（302 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) XYP beta-D-xylopyranose × 3 XYS alpha-D-xylopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.4；CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 1.9M (NH4)2SO4, 0.1M TRISHCL PH 8.4 AT 4 C
Resolution 2.40 Å R-free 0.274

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name XYNA_PENSI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–302； UniProt 2–302

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 1bg4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bg4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1bg4
Deposition date deposition_date1998-06-05
Structure title titleXYLANASE FROM PENICILLIUM SIMPLICISSIMUM
Keywords keywordsFAMILY 10 XYLANASE, PENICILLIUM SIMPLICISSIMUM, TIM-BARREL, GLYCOSYL HYDROLASE; FAMILY 10 XYLANASE
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_guinier19.46 Å
Radius of gyration Rg (electron density) rg_electron18.31 Å
Forward intensity I(0) i018879400.00
Molecular weight molecular_weight33562.0 kDa
Excluded volume excluded_volume42146 ų
Envelope volume envelope_volume44758 ų
Hydration-shell volume shell_volume20110 ų
Envelope diameter envelope_diameter62.0 Å
Shell Rg shell_rg25.03 Å
Envelope Rg envelope_rg18.49 Å
Shape Rg shape_rg18.29 Å
Total Rg total_rg19.26 Å
Total atoms total_atoms2362
Residues n_residues301
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 dmax62.7 Å
Rg (real space) rg_real19.34 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real1.8880e+07
I(0) uncertainty (real space) i0_real_error2.0980e+05
Rg (reciprocal space) rg_reciprocal19.36 Å
I(0) (reciprocal space) i0_reciprocal18880000.0000
Solution quality estimate total_estimate0.8885
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.8 Å
Skewness Skewness skewness0.184
Kurtosis Kurtosis kurtosis-0.401
Angular range angular_range— – 0.4100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4723000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1bg4a_
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 (1 domains)

Domain ID domain_id1bg4A00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
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8. Citations (1)

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9. Files and Curves (10)