SAXSdb — 1w2p

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

ENDO-1,4-BETA-XYLANASE A PRECURSOR

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 265–609 Chain A； UniProt 610–611	Fragment：CATALYTIC DOMAIN, RESIDUES 265-611	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.45 Å R-free 0.152
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 265–609 Chain B； UniProt 610–611	Fragment：CATALYTIC DOMAIN, RESIDUES 265-611	CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.45 Å R-free 0.152

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 1W2P	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 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 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 mutation/modification 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 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
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
1XYS CATALYTIC CORE OF XYLANASE A E246C MUTANT Deposited 1994-09-02	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）	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 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 2–346； UniProt 265–609 Author chain A； PDBConstruct 347–348； UniProt 610–611 Author chain B； PDBConstruct 2–346； UniProt 265–609 Author chain B； PDBConstruct 347–348； UniProt 610–611

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	1w2p
Deposition date deposition_date	2004-07-07
Structure title title	The 3-dimensional structure of a xylanase (Xyn10A) from Cellvibrio japonicus
Keywords keywords	XYLANASE, CALCIUM ION, THERMOSTABLE, GLYCOSYLE HYDROLASE, FAMILY 10, ERROR PRONE PCR, 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	29.53 Å
Radius of gyration Rg (electron density) rg_electron	28.52 Å
Forward intensity I(0) i0	101127000.00
Molecular weight molecular_weight	76751.0 kDa
Excluded volume excluded_volume	94787 Å³
Envelope volume envelope_volume	113150 Å³
Hydration-shell volume shell_volume	33342 Å³
Envelope diameter envelope_diameter	101.6 Å
Shell Rg shell_rg	35.52 Å
Envelope Rg envelope_rg	28.55 Å
Shape Rg shape_rg	28.50 Å
Total Rg total_rg	29.19 Å
Total atoms total_atoms	5420
Residues n_residues	692
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	99.0 Å
Rg (real space) rg_real	29.54 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	1.0110e+08
I(0) uncertainty (real space) i0_real_error	1.6680e+06
Rg (reciprocal space) rg_reciprocal	29.54 Å
I(0) (reciprocal space) i0_reciprocal	101100000.0000
Solution quality estimate total_estimate	0.8114
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	31.1 Å
Skewness Skewness skewness	0.334
Kurtosis Kurtosis kurtosis	-0.519
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29280000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ENDO-1,4-BETA-XYLANASE A PRECURSOR
Molecular weight formula_weight	38591.7 kDa
EC 编号 ec_number	3.2.1.8
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7933

MGLASLADFPIGVAVAASGGNADIFTSSARQNIVRAEFNQITAENIMKMSYMYSGSNFSFTNSDRLVSWAAQNGQTVHGHALVWHPSYQLPNWASDSNANFRQDFARHIDTVAAHFAGQVKSWDVVNEALFDSADDPDGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAADPTAELYYNDFNTEENGAKTTALVNLVQRLLNNGVPIDGVGFQMHVMNDYPSIANIRQAMQKIVALSPTLKIKITELDVRLNNPYDGNSSNDYTNRNDCAVSCAGLDRQKARYKEIVQAYLEVVPPGRRGGITVWGIADPDSWLYTHQNLPDWPLLFNDNLQPKPAYQGVVEALSGR

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	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	896

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1w2pa_
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	d1w2pb_
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 (2 domains)

Domain ID domain_id	1w2pA00
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	1w2pB00
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 (1)

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Unit-cell length a length_a	95.653 Å
Unit-cell length b length_b	95.653 Å
Unit-cell length c length_c	150.205 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	24.620 Å
R factor r_factor	0.1290
R_work r_work	0.1270
R_free r_free	0.1520

fit	/app/data/saxs_computation/w2/1w2p/1w2p.fit
pddf	/app/data/pr_computation/w2/1w2p/1w2p.pr.out
profile	/app/data/saxs_computation/w2/1w2p/1w2p.dat

The 3-dimensional structure of a xylanase (Xyn10A) from Cellvibrio japonicus

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

ENDO-1,4-BETA-XYLANASE A PRECURSOR

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