SAXSdb — 2z8r

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

YesW protein

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 10 (4S)-2-METHYL-2,4-PENTANEDIOL × 6 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 10 (4S)-2-METHYL-2,4-PENTANEDIOL × 4 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 20 (4S)-2-METHYL-2,4-PENTANEDIOL × 10 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O31526_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–583； UniProt 38–620 Author chain B； PDBConstruct 1–583； UniProt 38–620

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	2z8r
Deposition date deposition_date	2007-09-10
Structure title title	Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution
Keywords keywords	BETA-PROPELLER, LYASE; LYASE
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.

2z8r__assembly_1__model_1

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

Download this curve (.dat)

2z8r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2z8r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.10 Å
Rg (electron density)	23.05 Å
Total Rg	23.92 Å
Atom count	4531
Residues	583
Excluded volume	79956 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2z8r__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2z8r__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2z8r__assembly_3__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	YesW protein
Molecular weight formula_weight	64520.1 kDa
EC 编号 ec_number	4.2.2.-
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	11113

AARQMEALNRGLVAVKTDGGIFVSWRFLGTENASVLFNVYRDGQKLNAAPVKTTNYVDKNGSAGSTYTVRAVVNGTEQPASEKASVWAQPYHSVPLDKPAGGTTPKGESYTYSANDASVGDVDGDGQYELILKWDPSNSKDNSQDGYTGDVLIDAYKLDGTKLWRINLGKNIRAGAHYTQFMVYDLDGDGKAEVAMKTADGTKDGTGKVIGNANADYRNEQGRVLSGPEYLTVFQGSTGKELVTANFEPARGNVSDWGDSYGNRVDRFLAGIAYLDGQRPSLIMTRGYYAKTMLVAYNFRDGKLSKLWTLDSSKSGNEAFAGQGNHNLSIADVDGDGKDEIIFGSMAVDHDGKGMYSTGLGHGDALHTGDLDPGRPGLEVFQVHEDKNAKYGLSFRDAATGKILWGVYAGKDVGRGMAADIDPRYPGQEVWANGSLYSAKGVKIGSGVPSSTNFGIWWDGDLLREQLDSNRIDKWDYQNGVSKNMLTASGAAANNGTKATPTLQADLLGDWREEVVWRTEDSSALRIYTTTIPTEHRLYTLMHDPVYRLGIAWQNIAYNQPPHTSFFLGDGMAEQPKPNMYTPLEHHHHHH

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism 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	20

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1329

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2z8rA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2z8rB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	56.897 Å
Unit-cell length b length_b	106.153 Å
Unit-cell length c length_c	101.041 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.11 °
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	1.400 Å
Low-resolution limit resolution_low	28.400 Å
R factor r_factor	0.1645
R_work r_work	0.1635
R_free r_free	0.1822

Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution

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

YesW protein

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

2z8r__assembly_1__model_1

2z8r__assembly_1__model_1 | I(q)

2z8r__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution

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

YesW protein

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

2z8r__assembly_1__model_1

2z8r__assembly_1__model_1 | I(q)

2z8r__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)