SAXSdb — 3r9m

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

BRO1 domain-containing protein BROX

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–374	Fragment：UNP residues 2-374	EDO 1,2-ETHANEDIOL × 8 FMT FORMIC ACID × 11	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.1M MES, 1M sodium formate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.95 Å R-free 0.167

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3R9M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ULY Crystal Structure of BROX Bro1 Domain in Complex with the C-Terminal Tails of CHMP5 Deposited 2011-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–411（410 aa） Fragment：brox bro1 domain 2-411	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.211
3ULY Crystal Structure of BROX Bro1 Domain in Complex with the C-Terminal Tails of CHMP5 Deposited 2011-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–411（410 aa） Fragment：brox bro1 domain 2-411	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.211
3UM0 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5 Deposited 2011-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–411（410 aa） Fragment：Brox bro1 domain 2-411	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.10 Å R-free 0.257
3UM0 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5 Deposited 2011-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–411（410 aa） Fragment：Brox bro1 domain 2-411	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.10 Å R-free 0.257
3UM1 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5 Deposited 2011-11-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–377（376 aa） Fragment：Brox bro1 domain 2-377 Chain D 2–377（376 aa） Fragment：Brox bro1 domain 2-377	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.71 Å R-free 0.251
3UM2 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP5 Deposited 2011-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–377（376 aa） Fragment：Brox bro1 domain 2-377 Chain D 2–377（376 aa） Fragment：Brox bro1 domain 2-377	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.59 Å R-free 0.241
3UM3 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP4B Deposited 2011-11-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–411（410 aa） Fragment：Brox bro1 domain 2-377	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；273 K；1.0M sodium citrate, 0.1M imidazol, 15% glycerol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 3.80 Å R-free 0.243
3ZXP Structural and Functional Analyses of the Bro1 Domain Protein BROX Deposited 2011-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–401（401 aa） Fragment：BRO1, RESIDUES 1-401 Chain B 1–401（401 aa） Fragment：BRO1, RESIDUES 1-401 Chain C 1–401（401 aa） Fragment：BRO1, RESIDUES 1-401	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.6；22% PEG 1500, 0.1M MMT 6.6	Resolution 2.50 Å R-free 0.247

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BROX_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–376； UniProt 2–374

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	3r9m
Deposition date deposition_date	2011-03-25
Structure title title	Crystal structure of the Brox Bro1 domain
Keywords keywords	Bro1 domain, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.82 Å
Radius of gyration Rg (electron density) rg_electron	24.37 Å
Forward intensity I(0) i0	30679200.00
Molecular weight molecular_weight	43393.0 kDa
Excluded volume excluded_volume	54555 Å³
Envelope volume envelope_volume	63851 Å³
Hydration-shell volume shell_volume	23390 Å³
Envelope diameter envelope_diameter	95.8 Å
Shell Rg shell_rg	29.89 Å
Envelope Rg envelope_rg	24.86 Å
Shape Rg shape_rg	24.35 Å
Total Rg total_rg	25.08 Å
Total atoms total_atoms	3057
Residues n_residues	376
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	92.5 Å
Rg (real space) rg_real	25.12 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	3.0680e+07
I(0) uncertainty (real space) i0_real_error	4.6010e+05
Rg (reciprocal space) rg_reciprocal	25.05 Å
I(0) (reciprocal space) i0_reciprocal	30680000.0000
Solution quality estimate total_estimate	0.7803
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.672
Kurtosis Kurtosis kurtosis	0.154
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7373000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.547; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.555; Smooth: 0.944

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	BRO1 domain-containing protein BROX
Molecular weight formula_weight	42461.2 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	3558

GVDTHWFHRNPLKATAPVSFNYYGVVTGPSASKICNDLRSSRARLLELFTDLSCNPEMMKNAADSYFSLLQGFINSLDESTQESKLRYIQNFKWTDTLQGQVPSAQQDAVFELISMGFNVALWYTKYASRLAGKENITEDEAKEVHRSLKIAAGIFKHLKESHLPKLITPAEKGRDLESRLIEAYVIQCQAEAQEVTIARAIELKHAPGLIAALAYETANFYQKADHTLSSLEPAYSAKWRKYLHLKMCFYTAYAYCYHGETLLASDKCGEAIRSLQEAEKLYAKAEALCKEYGETKGPGPTVKPSGHLFFRKLGNLVKNTLEKCQRENGFIYFQKIPTEAPQLELKANYGLVEPIPFEFPPTSVQWTPETLAAFD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	452

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3r9mA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	280 — alix/aip1 like domains

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8. Citations (1)

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Unit-cell length a length_a	189.204 Å
Unit-cell length b length_b	189.204 Å
Unit-cell length c length_c	49.523 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	47.301 Å
R factor r_factor	0.1494
R_work r_work	0.1489
R_free r_free	0.1671

fit	/app/data/saxs_computation/r9/3r9m/3r9m.fit
pddf	/app/data/pr_computation/r9/3r9m/3r9m.pr.out
profile	/app/data/saxs_computation/r9/3r9m/3r9m.dat

Crystal structure of the Brox Bro1 domain

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

BRO1 domain-containing protein BROX

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction