SAXSdb — 1clx

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

XYLANASE A

Cellvibrio japonicus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 265–611 Chain B； UniProt 265–611	Fragment：CATALYTIC CORE, RESIDUES 264 - 611	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 1.80 Å
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 265–611 Chain D； UniProt 265–611	Fragment：CATALYTIC CORE, RESIDUES 264 - 611	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 1.80 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 1CLX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 ligand/ion 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 ligand/ion 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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 265–609（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 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 mutation/modification 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	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 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 mutation/modification 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 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 265–611（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 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 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 265–611（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 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）	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 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）	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 1–347； UniProt 265–611 Author chain B； PDBConstruct 1–347； UniProt 265–611 Author chain C； PDBConstruct 1–347； UniProt 265–611 Author chain D； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1clx
Deposition date deposition_date	1995-08-31
Structure title title	CATALYTIC CORE OF XYLANASE A
Keywords keywords	XYLANASE, FAMILY-F XYLANASE FAMILY 10 GLYCOSYL-HYDROLASE; XYLANASE
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	36.12 Å
Radius of gyration Rg (electron density) rg_electron	35.61 Å
Forward intensity I(0) i0	379314000.00
Molecular weight molecular_weight	152900.0 kDa
Excluded volume excluded_volume	188850 Å³
Envelope volume envelope_volume	231970 Å³
Hydration-shell volume shell_volume	53432 Å³
Envelope diameter envelope_diameter	116.7 Å
Shell Rg shell_rg	42.80 Å
Envelope Rg envelope_rg	34.91 Å
Shape Rg shape_rg	35.60 Å
Total Rg total_rg	36.10 Å
Total atoms total_atoms	10800
Residues n_residues	1380
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	113.9 Å
Rg (real space) rg_real	36.02 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	3.7930e+08
I(0) uncertainty (real space) i0_real_error	6.4400e+06
Rg (reciprocal space) rg_reciprocal	36.09 Å
I(0) (reciprocal space) i0_reciprocal	379300000.0000
Solution quality estimate total_estimate	0.8331
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.4 Å
Skewness Skewness skewness	0.226
Kurtosis Kurtosis kurtosis	-0.555
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	104800000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	XYLANASE A
Molecular weight formula_weight	38460.5 kDa
EC 编号 ec_number	3.2.1.8
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11908

GLASLADFPIGVAVAASGGNADIFTSSARQNIVRAEFNQITAENIMKMSYMYSGSNFSFTNSDRLVSWAAQNGQTVHGHALVWHPSYQLPNWASDSNANFRQDFARHIDTVAAHFAGQVKSWDVVNEALFDSADDPDGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAADPTAELYYNDFNTEENGAKTTALVNLVQRLLNNGVPIDGVGFQMHVMNDYPSIANIRQAMQKIVALSPTLKIKITELDVRLNNPYDGNSSNDYTNRNDCAVSCAGLDRQKARYKEIVQAYLEVVPPGRRGGITVWGIADPDSWLYTHQNLPDWPLLFNDNLQPKPAYQGVVEALSGR

来源 Source

来源生物 organism	Cellvibrio japonicus
NCBI Class编号 ncbi_taxonomy_id	155077
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1108

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1clxa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.3 — beta-glycanases

Domain ID domain_id	d1clxb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.3 — beta-glycanases

Domain ID domain_id	d1clxc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.3 — beta-glycanases

Domain ID domain_id	d1clxd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.3 — beta-glycanases

CATH v4.4 (4 domains)

Domain ID domain_id	1clxA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1clxB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1clxC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1clxD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

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8. Citations (4)

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Unit-cell length a length_a	96.110 Å
Unit-cell length b length_b	97.320 Å
Unit-cell length c length_c	151.030 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1660
R_free r_free	—

fit	/app/data/saxs_computation/cl/1clx/1clx.fit
pddf	/app/data/pr_computation/cl/1clx/1clx.pr.out
profile	/app/data/saxs_computation/cl/1clx/1clx.dat

CATALYTIC CORE OF XYLANASE A

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

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