SAXSdb — 1yrz

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

xylan beta-1,4-xylosidase

Bacillus halodurans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9K6P5_BACHD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–528； UniProt 1–528 Author chain B； PDBConstruct 1–528； UniProt 1–528

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	1yrz
Deposition date deposition_date	2005-02-05
Structure title title	Crystal structure of xylan beta-1,4-xylosidase from Bacillus Halodurans C-125
Keywords keywords	;Structural genomics, NYSGXRC target T1997, xylosidase, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGRC, 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.

1yrz__assembly_1__model_1

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

Download this curve (.dat)

1yrz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yrz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.71 Å
Rg (electron density)	23.83 Å
Total Rg	24.64 Å
Atom count	4229
Residues	522
Excluded volume	74341 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yrz__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yrz__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 (2)

Entity 1 Entity 1 polymer

Description description	xylan beta-1,4-xylosidase
Molecular weight formula_weight	60561.5 kDa
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	8867

MVNRIQNPILPGFHPDPSIVRVGDDYYIATSTFEWFPGVRIHHSRDLKHWRFVSSPLTRTSQLDMKGNMNSGGIWAPCLSYHDGTFYLIYTDVKQWHGAFKDAHNYLVTAQNIEGPWSDPIYLNSSGFDPSLFHDDDGRKWLVNMIWDYRKGNHPFAGIILQEYSEAEQKLVGPVKNIYKGTDIQLTEGPHLYKKDGYYYLLVAEGGTEYEHAATLARSQSIDGPYETDPSYPLVTSTGQPELALQKAGHGSLVETQNGEWYLAHLCGRPLKGKYCTLGRETAIQKVNWTEDGWLRIEDGGNHPLREVTAPDLPEHPFEKEPELDDFDAPQLHHQWNTLRIPADPSWCSLEERPGHLRLRGMESLTSVHSQSLVARRQQSFHCEVETKLEYQPESFQHMAGLVIYYDTEDHVYLHVTWHEEKGKCLQIIQTKGGNYDELLASPIPLAEEKAVYLKGRIHRETMHLYFKQEGEAEWQPVGPTIDVTHMSDDSAKQVRFTGTFVGMATQDLSGTKKPADFDYFRYKELDQ

Source Source

Source organism organism	Bacillus halodurans
NCBI taxonomy ID ncbi_taxonomy_id	272558
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	409

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1yrza1
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.29.1.23 — Beta-D-xylosidase C-terminal domain-like

Domain ID domain_id	d1yrza2
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.1 — alpha-L-arabinanase-like

Domain ID domain_id	d1yrzb1
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.29.1.23 — Beta-D-xylosidase C-terminal domain-like

Domain ID domain_id	d1yrzb2
Class class	b — All beta proteins
Fold Fold fold	b.67 — 5-bladed beta-propeller
Superfamily Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
Family Family family	b.67.2.1 — alpha-L-arabinanase-like

CATH v4.4 (4 domains)

Domain ID domain_id	1yrzA01
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	1yrzA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1yrzB01
Class class	2 — Mainly Beta
Architecture architecture	115 — 5 Propeller
Topology topology	10 — Tachylectin-2; Chain A
Homologous superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

Domain ID domain_id	1yrzB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

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Unit-cell length a length_a	54.063 Å
Unit-cell length b length_b	125.817 Å
Unit-cell length c length_c	97.131 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.08 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	24.870 Å
R factor r_factor	0.2090
R_work r_work	0.2070
R_free r_free	0.2240

Crystal structure of xylan beta-1,4-xylosidase from Bacillus Halodurans C-125

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

xylan beta-1,4-xylosidase

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

1yrz__assembly_1__model_1

1yrz__assembly_1__model_1 | I(q)

1yrz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of xylan beta-1,4-xylosidase from Bacillus Halodurans C-125

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

xylan beta-1,4-xylosidase

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

1yrz__assembly_1__model_1

1yrz__assembly_1__model_1 | I(q)

1yrz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)