SAXSdb — 3e38

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

two-domain protein containing predicted PHP-like metal-dependent phosphoesterase

Bacteroides vulgatus ATCC 8482

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 12 CACODYLATE ION × 4 GLYCEROL × 6 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A6L615_BACV8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–343； UniProt 22–363 Author chain B； PDBConstruct 2–343； UniProt 22–363

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	3e38
Deposition date deposition_date	2008-08-06
Structure title title	CRYSTAL STRUCTURE OF A TWO-DOMAIN PROTEIN CONTAINING PREDICTED PHP-LIKE METAL-DEPENDENT PHOSPHOESTERASE (BVU_3505) FROM BACTEROIDES VULGATUS ATCC 8482 AT 2.20 A RESOLUTION
Keywords keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, 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.

3e38__assembly_1__model_1

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

Download this curve (.dat)

3e38__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3e38__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.50 Å
Rg (electron density)	33.65 Å
Total Rg	34.18 Å
Atom count	11070
Residues	1338
Excluded volume	196530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3e38__assembly_1__model_1`	tetrameric （4）	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	two-domain protein containing predicted PHP-like metal-dependent phosphoesterase
Molecular weight formula_weight	40015.0 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	6016

GAQRRNEIQVPDLDGYTTLKCDFHMHSVFSDGLVWPTVRVDEAYRDGLDAISLTEHIEYRPHKQDVVSDHNRSFDLCREQAEKLGILLIKGSEITRAMAPGHFNAIFLSDSNPLEQKDYKDAFREAKKQGAFMFWNHPGWDSQQPDTTKWWPEHTALYQEGCMHGIEVANGHLYMPEAIQWCLDKNLTMIGTSDIHQPIQTDYDFEKGEHRTMTFVFAKERSLQGIREALDNRRTAAYFHELLIGREDLLRPFFEKCVKIEEVSRNEQGVTLSITNVTDLVLKLKKTAHDTLLVYFRDMTLKPHTRYTVRIGFKQGIKGGDVNFEVTNFIVAPDKGLKYTISL

Source Source

Source organism organism	Bacteroides vulgatus ATCC 8482
NCBI taxonomy ID ncbi_taxonomy_id	435590
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
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	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	431

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3e38A01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	3e38A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3090 —

Domain ID domain_id	3e38B01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	3e38B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3090 —

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Unit-cell length a length_a	95.680 Å
Unit-cell length b length_b	117.820 Å
Unit-cell length c length_c	79.560 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	29.604 Å
R factor r_factor	0.1750
R_work r_work	0.1720
R_free r_free	0.2250

CRYSTAL STRUCTURE OF A TWO-DOMAIN PROTEIN CONTAINING PREDICTED PHP-LIKE METAL-DEPENDENT PHOSPHOESTERASE (BVU_3505) FROM BACTEROIDES VULGATUS ATCC 8482 AT 2.20 A RESOLUTION

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

two-domain protein containing predicted PHP-like metal-dependent phosphoesterase

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

3e38__assembly_1__model_1

3e38__assembly_1__model_1 | I(q)

3e38__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A TWO-DOMAIN PROTEIN CONTAINING PREDICTED PHP-LIKE METAL-DEPENDENT PHOSPHOESTERASE (BVU_3505) FROM BACTEROIDES VULGATUS ATCC 8482 AT 2.20 A RESOLUTION

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

two-domain protein containing predicted PHP-like metal-dependent phosphoesterase

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

3e38__assembly_1__model_1

3e38__assembly_1__model_1 | I(q)

3e38__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)