SAXSdb — 3d1l

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

Putative NADP oxidoreductase BF3122

Bacteroides fragilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-MERCAPTO-PROPION ALDEHYDE × 2 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5LAQ6_BACFN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–266； UniProt 1–263 Author chain B； PDBConstruct 4–266； UniProt 1–263

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	3d1l
Deposition date deposition_date	2008-05-06
Structure title title	Crystal structure of putative NADP oxidoreductase BF3122 from Bacteroides fragilis
Keywords keywords	;putative NADP oxidoreductase, BF3122, Bacteroides fragilis, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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.

3d1l__assembly_1__model_1

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

Download this curve (.dat)

3d1l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d1l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.92 Å
Rg (electron density)	28.55 Å
Total Rg	28.83 Å
Atom count	4090
Residues	502
Excluded volume	73197 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d1l__assembly_1__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	Putative NADP oxidoreductase BF3122
Molecular weight formula_weight	30502.5 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	4447

SNAMKRSIEDTPIVLIGAGNLATNLAKALYRKGFRIVQVYSRTEESARELAQKVEAEYTTDLAEVNPYAKLYIVSLKDSAFAELLQGIVEGKREEALMVHTAGSIPMNVWEGHVPHYGVFYPMQTFSKQREVDFKEIPFFIEASSTEDAAFLKAIASTLSNRVYDADSEQRKSLHLAAVFTCNFTNHMYALAAELLKKYNLPFDVMLPLIDETARKVHELEPKTAQTGPAIRYDENVIGNHLRMLADDPAMQRLYELLSRSIHERQ

Source Source

Source organism organism	Bacteroides fragilis
NCBI taxonomy ID ncbi_taxonomy_id	272559
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-MERCAPTO-PROPION ALDEHYDE
Molecular weight formula_weight	90.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	231

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3d1lA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3d1lA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Homologous superfamily homologous superfamily	20 — ProC-like, C-terminal domain

Domain ID domain_id	3d1lB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3d1lB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Homologous superfamily homologous superfamily	20 — ProC-like, C-terminal domain

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Unit-cell length a length_a	154.995 Å
Unit-cell length b length_b	154.995 Å
Unit-cell length c length_c	54.313 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	16

Space group space_group	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	2.190 Å
Low-resolution limit resolution_low	33.710 Å
R factor r_factor	0.1880
R_work r_work	0.1853
R_free r_free	0.2391

Crystal structure of putative NADP oxidoreductase BF3122 from Bacteroides fragilis

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

Putative NADP oxidoreductase BF3122

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

3d1l__assembly_1__model_1

3d1l__assembly_1__model_1 | I(q)

3d1l__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of putative NADP oxidoreductase BF3122 from Bacteroides fragilis

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

Putative NADP oxidoreductase BF3122

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

3d1l__assembly_1__model_1

3d1l__assembly_1__model_1 | I(q)

3d1l__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)