SAXSdb — 2dcy

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

Endo-1,4-beta-xylanase A

Bacillus subtilis

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 29–213	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 1 TLA L(+)-TARTARIC ACID × 1 TAR D(-)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.1M Imidazole, 1.0-1.1K/Na tartrate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.217
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 29–213	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 1 TLA L(+)-TARTARIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.1M Imidazole, 1.0-1.1K/Na tartrate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.217
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 29–213	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 1 TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.1M Imidazole, 1.0-1.1K/Na tartrate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.217
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 29–213	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.1M Imidazole, 1.0-1.1K/Na tartrate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.217
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 29–213	Not recorded	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；0.1M Imidazole, 1.0-1.1K/Na tartrate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.217

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 2DCY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AXK ENGINEERED BACILLUS BIFUNCTIONAL ENZYME GLUXYN-1 Deposited 1997-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–213（185 aa） Fragment：FUSION OF 1,3-1,4-BETA-GLUCANASE DOMAIN AND 1,4-BETA-XYLANASE DOMAIN Chain B 29–213（185 aa） Fragment：FUSION OF 1,3-1,4-BETA-GLUCANASE DOMAIN AND 1,4-BETA-XYLANASE DOMAIN	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.10 Å R-free 0.224
1XXN Crystal structure of a mesophilic xylanase A from Bacillus subtilis 1A1 Deposited 2004-11-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Not recorded	SRT S,R MESO-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；0.9M sodium tartrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.212
2B42 Crystal structure of the Triticum xylanse inhibitor-I in complex with bacillus subtilis xylanase Deposited 2005-09-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 29–213（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；0.22 M ammonium sulphate, 0.1 M sodium acetate buffer, 25 % (w/v) polyethylene glycol 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.240
2B45 Crystal structure of an engineered uninhibited Bacillus subtilis xylanase in free state Deposited 2005-09-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 29–213（185 aa）	Mutation：D11F/R122D	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20 % (w/v) polyethylene glycol 8000, 0.1 M HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.195
2B46 Crystal structure of an engineered uninhibited Bacillus subtilis xylanase in substrate bound state Deposited 2005-09-22	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain X 29–213（185 aa）	Mutation：D11F/R122D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；20 % (w/v) polyethylene glycol 8000, 0.1 M HEPES buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.21 Å R-free 0.198
2DCZ Thermal Stabilization of Bacillus subtilis Family-11 Xylanase By Directed Evolution Deposited 2006-01-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：Q7H, N8F, S179C	SO4 SULFATE ION × 1 DIO 1,4-DIETHYLENE DIOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES, 1.1-1.2M ammonium sulfate, 10% deoxane, 25mM DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.223
2DCZ Thermal Stabilization of Bacillus subtilis Family-11 Xylanase By Directed Evolution Deposited 2006-01-18	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：Q7H, N8F, S179C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES, 1.1-1.2M ammonium sulfate, 10% deoxane, 25mM DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.223
2DCZ Thermal Stabilization of Bacillus subtilis Family-11 Xylanase By Directed Evolution Deposited 2006-01-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 29–213（185 aa）	Mutation：Q7H, N8F, S179C	SO4 SULFATE ION × 3 DIO 1,4-DIETHYLENE DIOXIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES, 1.1-1.2M ammonium sulfate, 10% deoxane, 25mM DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.223
2QZ3 Crystal structure of a glycoside hydrolase family 11 xylanase from Bacillus subtilis in complex with xylotetraose Deposited 2007-08-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E172A	ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2M ammonium sulphate, 0.1M Tris-HCl pH 8.5, 30% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.188
2QZ3 Crystal structure of a glycoside hydrolase family 11 xylanase from Bacillus subtilis in complex with xylotetraose Deposited 2007-08-16	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 29–213（185 aa）	Mutation：E172A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2M ammonium sulphate, 0.1M Tris-HCl pH 8.5, 30% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.188
2Z79 High resolution crystal structure of a glycoside hydrolase family 11 xylanase of Bacillus subtilis Deposited 2007-08-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E172A	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M imidazole pH 6.5, 1.0M sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.30 Å R-free 0.176
2Z79 High resolution crystal structure of a glycoside hydrolase family 11 xylanase of Bacillus subtilis Deposited 2007-08-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：E172A	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M imidazole pH 6.5, 1.0M sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.30 Å R-free 0.176
3HD8 Crystal structure of the Triticum aestivum xylanase inhibitor-IIA in complex with bacillus subtilis xylanase Deposited 2009-05-07	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 29–213（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；18% (w/v) polyethylene glycol 4000, 0.18M ammonium sulfate, 0.1M sodium acetate buffer , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.39 Å R-free 0.275
3HD8 Crystal structure of the Triticum aestivum xylanase inhibitor-IIA in complex with bacillus subtilis xylanase Deposited 2009-05-07	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 29–213（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；18% (w/v) polyethylene glycol 4000, 0.18M ammonium sulfate, 0.1M sodium acetate buffer , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.39 Å R-free 0.275
5K9Y Crystal structure of a thermophilic xylanase A from Bacillus subtilis 1A1 quadruple mutant Q7H/G13R/S22P/S179C Deposited 2016-06-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa） Fragment：residues 29-213	Mutation：Q7H, G13R, S22P, S179C Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.1 M HEPES and 0.6 M sodium tartrate	Resolution 2.20 Å R-free 0.248
5K9Y Crystal structure of a thermophilic xylanase A from Bacillus subtilis 1A1 quadruple mutant Q7H/G13R/S22P/S179C Deposited 2016-06-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa） Fragment：residues 29-213	Mutation：Q7H, G13R, S22P, S179C Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.1 M HEPES and 0.6 M sodium tartrate	Resolution 2.20 Å R-free 0.248
5TVV Computationally Designed Fentanyl Binder - Fen49* Apo Deposited 2016-11-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–213（184 aa） Fragment：UNP residues 30-213	Mutation：Y88A	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.8M sodium phosphate, 0.8M potassium phosphate, 0.1M HEPES pH 7.5	Resolution 1.79 Å R-free 0.225
5TVV Computationally Designed Fentanyl Binder - Fen49* Apo Deposited 2016-11-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 30–213（184 aa） Fragment：UNP residues 30-213	Mutation：Y88A	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.8M sodium phosphate, 0.8M potassium phosphate, 0.1M HEPES pH 7.5	Resolution 1.79 Å R-free 0.225
5TVV Computationally Designed Fentanyl Binder - Fen49* Apo Deposited 2016-11-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 30–213（184 aa） Fragment：UNP residues 30-213	Mutation：Y88A	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.8M sodium phosphate, 0.8M potassium phosphate, 0.1M HEPES pH 7.5	Resolution 1.79 Å R-free 0.225
5TVY Computationally Designed Fentanyl Binder - Fen49 Deposited 2016-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–213（184 aa） Fragment：UNP residues 30-213	Not recorded	XPE 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.5；293.15 K；1ul of protein at 20mg/ml mixed with 1ul of mother liquor, plus 0.2ul of a seed stock made from a previous crystallization drop. Crystallization condition is 0.1M Citric Acid pH 3.5, 25% PEG 3350.	Resolution 1.00 Å R-free 0.121
5TVY Computationally Designed Fentanyl Binder - Fen49 Deposited 2016-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 30–213（184 aa） Fragment：UNP residues 30-213	Not recorded	XPE 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.5；293.15 K；1ul of protein at 20mg/ml mixed with 1ul of mother liquor, plus 0.2ul of a seed stock made from a previous crystallization drop. Crystallization condition is 0.1M Citric Acid pH 3.5, 25% PEG 3350.	Resolution 1.00 Å R-free 0.121
5TZO Computationally Designed Fentanyl Binder - Fen49*-Complex Deposited 2016-11-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–213（184 aa） Fragment：UNP residues 30-213	Not recorded	7V7 N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide × 2 K POTASSIUM ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.8M sodium phosphate, 0.8M potassium phosphate, 0.1M HEPES pH 7.5	Resolution 1.67 Å R-free 0.203
5TZO Computationally Designed Fentanyl Binder - Fen49*-Complex Deposited 2016-11-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 30–213（184 aa） Fragment：UNP residues 30-213	Not recorded	7V7 N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide × 2 K POTASSIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.8M sodium phosphate, 0.8M potassium phosphate, 0.1M HEPES pH 7.5	Resolution 1.67 Å R-free 0.203
5TZO Computationally Designed Fentanyl Binder - Fen49*-Complex Deposited 2016-11-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 30–213（184 aa） Fragment：UNP residues 30-213	Not recorded	7V7 N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.8M sodium phosphate, 0.8M potassium phosphate, 0.1M HEPES pH 7.5	Resolution 1.67 Å R-free 0.203

13 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	XYNA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–185； UniProt 29–213 Author chain B； PDBConstruct 1–185； UniProt 29–213 Author chain C； PDBConstruct 1–185； UniProt 29–213 Author chain D； PDBConstruct 1–185； UniProt 29–213 Author chain E； PDBConstruct 1–185； UniProt 29–213

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	2dcy
Deposition date deposition_date	2006-01-18
Structure title title	Crystal structure of Bacillus subtilis family-11 xylanase
Keywords keywords	ALL BETA, HYDROLASE; 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	33.84 Å
Radius of gyration Rg (electron density) rg_electron	33.28 Å
Forward intensity I(0) i0	180573000.00
Molecular weight molecular_weight	103240.0 kDa
Excluded volume excluded_volume	126760 Å³
Envelope volume envelope_volume	155880 Å³
Hydration-shell volume shell_volume	40576 Å³
Envelope diameter envelope_diameter	112.4 Å
Shell Rg shell_rg	38.66 Å
Envelope Rg envelope_rg	32.85 Å
Shape Rg shape_rg	33.27 Å
Total Rg total_rg	33.70 Å
Total atoms total_atoms	7323
Residues n_residues	925
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	110.8 Å
Rg (real space) rg_real	33.83 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	1.8060e+08
I(0) uncertainty (real space) i0_real_error	3.0680e+06
Rg (reciprocal space) rg_reciprocal	33.84 Å
I(0) (reciprocal space) i0_reciprocal	180600000.0000
Solution quality estimate total_estimate	0.8937
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.8 Å
Skewness Skewness skewness	0.273
Kurtosis Kurtosis kurtosis	-0.520
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	67950000.0000
Real-space data points n_real_points	48
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: 0.957; Smooth: 0.920

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Endo-1,4-beta-xylanase A
Molecular weight formula_weight	20395.0 kDa
EC 编号 ec_number	3.2.1.8
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	7611

ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFSNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,4-DIETHYLENE DIOXIDE
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	D(-)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	248

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2dcya_
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

Domain ID domain_id	d2dcyb_
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

Domain ID domain_id	d2dcyc_
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

Domain ID domain_id	d2dcyd_
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

Domain ID domain_id	d2dcye_
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 (5 domains)

Domain ID domain_id	2dcyA00
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

Domain ID domain_id	2dcyB00
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

Domain ID domain_id	2dcyC00
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

Domain ID domain_id	2dcyD00
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

Domain ID domain_id	2dcyE00
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 (1)

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Unit-cell length a length_a	130.445 Å
Unit-cell length b length_b	186.209 Å
Unit-cell length c length_c	37.979 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	20

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1983
R_work r_work	0.1973
R_free r_free	0.2173

fit	/app/data/saxs_computation/dc/2dcy/2dcy.fit
pddf	/app/data/pr_computation/dc/2dcy/2dcy.pr.out
profile	/app/data/saxs_computation/dc/2dcy/2dcy.dat

Crystal structure of Bacillus subtilis family-11 xylanase

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

Endo-1,4-beta-xylanase A

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