SAXSdb — 2bry

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

NEDD9 INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS

MUS MUSCULUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 GLYCEROL × 1 SULFATE ION × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 SULFATE ION × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MICA1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–497； UniProt 1–489 Author chain B； PDBConstruct 9–497； UniProt 1–489

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	2bry
Deposition date deposition_date	2005-05-13
Structure title title	Crystal structure of the native monooxygenase domain of MICAL at 1.45 A resolution
Keywords keywords	TRANSPORT, COILED COIL, CYTOSKELETON, FAD, FLAVOPROTEIN, LIM DOMAIN, METAL-BINDING, ZINC; TRANSPORT
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.

2bry__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2bry__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bry__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.44 Å
Rg (electron density)	23.30 Å
Total Rg	24.20 Å
Atom count	3800
Residues	479
Excluded volume	67651 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bry__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2bry__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 (6)

Entity 1 Entity 1 polymer

Description description	NEDD9 INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS
Molecular weight formula_weight	55237.4 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	9235

MAHHHHHHMASPASTNPAHDHFETFVQAQLCQDVLSSFQGLCRALGVESGGGLSQYHKIKAQLNYWSAKSLWAKLDKRASQPVYQQGQACTNTKCLVVGAGPCGLRAAVELALLGARVVLVEKRIKFSRHNVLHLWPFTIHDLRALGAKKFYGRFCTGTLDHISIRQLQLLLLKVALLLGVEIHWGVKFTGLQPPPRKGSGWRAQLQPNPPAQLASYEFDVLISAAGGKFVPEGFTIREMRGKLAIGITANFVNGRTVEETQVPEISGVARIYNQKFFQSLLKATGIDLENIVYYKDETHYFVMTAKKQCLLRLGVLRQDLSETDQLLGKANVVPEALQRFARAAADFATHGKLGKLEFAQDARGRPDVAAFDFTSMMRAESSARVQEKHGARLLLGLVGDCLVEPFWPLGTGVARGFLAAFDAAWMVKRWAEGAGPLEVLAERESLYQLLSQTSPENMHRNVAQYGLDPATRYPNLNLRAVTPNQVQDLYDMMDKE

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1583

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2bryA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2bryB01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

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Unit-cell length a length_a	76.588 Å
Unit-cell length b length_b	89.548 Å
Unit-cell length c length_c	83.458 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.35 °
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	1.450 Å
Low-resolution limit resolution_low	76.030 Å
R factor r_factor	0.1810
R_work r_work	0.1800
R_free r_free	0.2220

Crystal structure of the native monooxygenase domain of MICAL at 1.45 A resolution

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

NEDD9 INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS

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

2bry__assembly_2__model_1

2bry__assembly_2__model_1 | I(q)

2bry__assembly_2__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the native monooxygenase domain of MICAL at 1.45 A resolution

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

NEDD9 INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS

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

2bry__assembly_2__model_1

2bry__assembly_2__model_1 | I(q)

2bry__assembly_2__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)