SAXSdb — 1bk1

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

ENDO-1,4-B-XYLANASE C

Aspergillus kawachii

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 28–211	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.00 Å R-free 0.260

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 1BK1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3RI8 Xylanase C from Aspergillus kawachii D37N mutant Deposited 2011-04-13	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–211（184 aa）	Mutation：D37N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.5M sodium sulfate, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.228
3RI9 Xylanase C from Aspergillus kawachii F131W mutant Deposited 2011-04-13	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–211（184 aa）	Mutation：F131W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.5M sodium sulfate, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.212

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

View Construct and Data Evidence

UniProt name	XYN3_ASPKA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–184； UniProt 28–211

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bk1
Deposition date deposition_date	1998-07-14
Structure title title	ENDO-1,4-BETA-XYLANASE C
Keywords keywords	HYDROLASE, XYLAN DEGRADATION, GLYCOSIDASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	16.17 Å
Radius of gyration Rg (electron density) rg_electron	14.78 Å
Forward intensity I(0) i0	7876180.00
Molecular weight molecular_weight	19684.0 kDa
Excluded volume excluded_volume	24065 Å³
Envelope volume envelope_volume	26006 Å³
Hydration-shell volume shell_volume	14610 Å³
Envelope diameter envelope_diameter	47.3 Å
Shell Rg shell_rg	20.95 Å
Envelope Rg envelope_rg	14.93 Å
Shape Rg shape_rg	14.75 Å
Total Rg total_rg	15.88 Å
Total atoms total_atoms	1394
Residues n_residues	182
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	48.4 Å
Rg (real space) rg_real	16.01 Å
Rg uncertainty (real space) rg_real_error	0.18 Å
I(0) (real space) i0_real	7.8760e+06
I(0) uncertainty (real space) i0_real_error	7.9570e+04
Rg (reciprocal space) rg_reciprocal	16.03 Å
I(0) (reciprocal space) i0_reciprocal	7876000.0000
Solution quality estimate total_estimate	0.8994
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.7 Å
Skewness Skewness skewness	-0.005
Kurtosis Kurtosis kurtosis	-0.509
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2093000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.985

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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 (1 domains)

Domain ID domain_id	d1bk1a_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.11 — Xylanase/endoglucanase 11/12

CATH v4.4 (1 domains)

Domain ID domain_id	1bk1A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	180 — Glycoside hydrolase family 11/12, catalytic domain

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8. Citations (3)

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Unit-cell length a length_a	62.065 Å
Unit-cell length b length_b	62.065 Å
Unit-cell length c length_c	113.291 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2600

Description description	ENDO-1,4-B-XYLANASE C
Molecular weight formula_weight	19894.0 kDa
EC 编号 ec_number	3.2.1.8
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1505

ENDO-1,4-BETA-XYLANASE C

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

ENDO-1,4-B-XYLANASE C

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Aspergillus kawachii
NCBI Class编号 ncbi_taxonomy_id	40384
宿主生物 host_organism	Aspergillus kawachii

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	111

fit	/app/data/saxs_computation/bk/1bk1/1bk1.fit
pddf	/app/data/pr_computation/bk/1bk1/1bk1.pr.out
profile	/app/data/saxs_computation/bk/1bk1/1bk1.dat