SAXSdb — 2d23

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

ENDO-1,4-BETA-D-XYLANASE

Streptomyces olivaceoviridis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose × 1 AZIDE ION × 1 GLYCEROL × 3 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose × 1 AZIDE ION × 1 GLYCEROL × 5 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7SI98_STROI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–436； UniProt 1–436 Author chain B； PDBConstruct 1–436； UniProt 1–436

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	2d23
Deposition date deposition_date	2005-09-02
Structure title title	Crystal structure of EP complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86
Keywords keywords	TIM-BARREL, RETAINING ENZYME, CATALYTIC-SITE MUTANT, CHEMICAL RESCUE, EP COMPLEX, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2d23__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2d23__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d23__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.21 Å
Rg (electron density)	24.60 Å
Total Rg	25.27 Å
Atom count	3272
Residues	427
Excluded volume	56787 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d23__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2d23__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	ENDO-1,4-BETA-D-XYLANASE
Molecular weight formula_weight	46773.2 kDa
EC 编号 ec_number	3.2.1.8
Mutation mutation	N127S and E128H
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	7304

AESTLGAAAAQSGRYFGTAIASGKLGDSAYTTIASREFNMVTAENEMKIDATEPQRGQFNFSAGDRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSTLRQAMIDHINGVMGHYKGKIAQWDVVSHAFSDDGSGGRRDSNLQRTGNDWIEVAFRTARAADPAAKLCYNDYNIENWTWAKTQGVYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGASSSTYAAVTNDCLAVSRCLGITVWGVRDTDSWRSGDTPLLFNGDGSKKAAYTAVLNALNGGSSTPPPSGGGQIKGVGSGRCLDVPNASTTDGTQVQLYDCHSATNQQWTYTDAGELRVYGDKCLDAAGTGNGTKVQIYSCWGGDNQKWRLNSDGSIVGVQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT

Source Source

Source organism organism	Streptomyces olivaceoviridis
NCBI taxonomy ID ncbi_taxonomy_id	1921
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	alpha-D-xylopyranose-(1-4)-alpha-D-xylopyranose
Molecular weight formula_weight	282.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	AZIDE ION
Molecular weight formula_weight	42.0 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	748

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2d23a1
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	d2d23a2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.0 — automated matches

Domain ID domain_id	d2d23b1
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	d2d23b2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2d23A01
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	2d23A02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2d23B01
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	2d23B02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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7. Citations (6)

Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86

J.Biochem. (2009)

PMID: 19279191 · DOI: 10.1093/jb/mvp047 PRIMARY

Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86

J.Biol.Chem. (2004)

PMID: 14670957 · DOI: 10.1074/jbc.M312293200

;Crystal structures of the sugar complexes of Streptomyces olivaceoviridis E-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module ;

J.Mol.Biol. (2002)

PMID: 11829503 · DOI: 10.1006/jmbi.2001.5338

Crystal structure of Streptomyces olivaceoviridis E-86 beta-xylanase containing xylan-binding domain

J.Mol.Biol. (2000)

PMID: 10884353 · DOI: 10.1006/jmbi.2000.3877

;Significant enhancement in the binding of p-nitrophenyl-beta-D-xylobioside by the E128H mutant F/10 xylanase from Streptomyces olivaceoviridis E-86 ;

Febs Lett. (1999)

PMID: 10359093 · DOI: 10.1016/S0014-5793(99)00498-6

PCR Cloning and Expression of the F/10 Family Xylanse Gene from Streptomyces olivaceoviridis E-86

J.FERMENT.BIOENG. (1998)

DOI: 10.1016/S0922-338X(98)80147-5

Unit-cell length a length_a	78.929 Å
Unit-cell length b length_b	94.092 Å
Unit-cell length c length_c	139.466 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	47.050 Å
R factor r_factor	0.1830
R_work r_work	0.1830
R_free r_free	0.2110

Crystal structure of EP complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86

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

ENDO-1,4-BETA-D-XYLANASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2d23__assembly_1__model_1

2d23__assembly_1__model_1 | I(q)

2d23__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (6)

Crystal structure of EP complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86

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

ENDO-1,4-BETA-D-XYLANASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2d23__assembly_1__model_1

2d23__assembly_1__model_1 | I(q)

2d23__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (6)