SAXSdb — 3cym

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

Uncharacterized protein BAD_0989

Bifidobacterium adolescentis ATCC 15703

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A1A237_BIFAA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–432； UniProt 2–430

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	3cym
Deposition date deposition_date	2008-04-25
Structure title title	Crystal structure of protein BAD_0989 from Bifidobacterium adolescentis
Keywords keywords	;STRUCTURAL GENOMICS, UNKNOWN FUNCTION, UNCHARACTERIZED PROTEIN, RIBONUCLEASE D, EXONUCLEASE, PROTEIN STRUCTURE INITIATIVE, PSI-2, New York SGX Research Center for Structural Genomics, NYSGXRC ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

3cym__assembly_1__model_1

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

Download this curve (.dat)

3cym__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cym__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.54 Å
Rg (electron density)	25.42 Å
Total Rg	26.29 Å
Atom count	3370
Residues	415
Excluded volume	59704 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cym__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Uncharacterized protein BAD_0989
Molecular weight formula_weight	50497.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3825

MSLTDEPKLLAEPREGVPNVIDTLPAFRDYCSELASSHGSLAADAERASGFRYGHEDWLVQFKRDGAGIGLLDPQALAAAGADWNDFNRAVGDAVWILHDSLQDLPGFDELGMEPQRLFDTEIAARLLGLKRFGLAAVTEHFLGLTLAKEHSAADWSYRPLPRDWRNYAALDVELLIELETKMRAELKRQGKMEWAQEEFDYALKEGLGPRKEHLIPWMHVSHITEVMRDRQALAIVRALWTRRDELAREYDIAPTLLLSDSSIIEVAKRKPHNAAQFRSIRSINERVRIHTDSEQDKMFERYAPIQRKIKPSMWKNIIQDALALPPSEWPDVDGGAARRHESQSASAPKSIRVWKERYPERLQVLNRVRKAVSQIAEDTRTPVEIVIKPQYLRNLCWTDEPRKRDVARFLSEQGARDWQVSLVAESVSRAIEGHHHHHH

Source Source

Source organism organism	Bifidobacterium adolescentis ATCC 15703
NCBI taxonomy ID ncbi_taxonomy_id	367928
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	290

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3cymA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	3cymA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	80 — HRDC domain

Domain ID domain_id	3cymA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	80 — HRDC domain

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Unit-cell length a length_a	42.163 Å
Unit-cell length b length_b	94.422 Å
Unit-cell length c length_c	113.196 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2242
R_work r_work	0.2218
R_free r_free	0.2940

Crystal structure of protein BAD_0989 from Bifidobacterium adolescentis

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

Uncharacterized protein BAD_0989

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

3cym__assembly_1__model_1

3cym__assembly_1__model_1 | I(q)

3cym__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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of protein BAD_0989 from Bifidobacterium adolescentis

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

Uncharacterized protein BAD_0989

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

3cym__assembly_1__model_1

3cym__assembly_1__model_1 | I(q)

3cym__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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)