SAXSdb — 2wp1

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

BROMODOMAIN TESTIS-SPECIFIC PROTEIN

MUS MUSCULUS

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 257–382	Fragment：BROMODOMAIN 2, RESIDUES 257-382	HISTONE H3 × 1 （B9EI85）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；BRDT BD2 PROTEIN AT 25 MG/ML WAS MIXED WITH H3-ACK18 PEPTIDE IN A 1:5 MOLAR RATIO. CRYSTALLIZATION WAS BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 2.0 M AMMONIUM SULFATE, 2% PEG 400, 0.1 M HEPES PH 7.5	Resolution 2.10 Å R-free 0.255
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 257–382	Fragment：BROMODOMAIN 2, RESIDUES 257-382	HISTONE H3 × 1 （B9EI85）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；BRDT BD2 PROTEIN AT 25 MG/ML WAS MIXED WITH H3-ACK18 PEPTIDE IN A 1:5 MOLAR RATIO. CRYSTALLIZATION WAS BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 2.0 M AMMONIUM SULFATE, 2% PEG 400, 0.1 M HEPES PH 7.5	Resolution 2.10 Å R-free 0.255

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 2WP1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2WP2 Structure of Brdt bromodomain BD1 bound to a diacetylated histone H4 peptide. Deposited 2009-08-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–136（120 aa） Fragment：BROMODOMAIN 1, RESIDUES 17-136	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；15 MG/ML BRDT-BD1 PROTEIN WAS MIXED WITH H4-ACK5/K8 PEPTIDE IN A 1:20 MOLAR RATIO. CRYSTALLIZATION WAS BY THE HANGING DROP VAPOUR DIFFUSION METHOD FROM 2.4 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.	Resolution 2.37 Å R-free 0.261
2WP2 Structure of Brdt bromodomain BD1 bound to a diacetylated histone H4 peptide. Deposited 2009-08-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 17–136（120 aa） Fragment：BROMODOMAIN 1, RESIDUES 17-136	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；15 MG/ML BRDT-BD1 PROTEIN WAS MIXED WITH H4-ACK5/K8 PEPTIDE IN A 1:20 MOLAR RATIO. CRYSTALLIZATION WAS BY THE HANGING DROP VAPOUR DIFFUSION METHOD FROM 2.4 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.	Resolution 2.37 Å R-free 0.261

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BRDT_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–126； UniProt 257–382 Author chain B； PDBConstruct 1–126； UniProt 257–382

HISTONE H3

OrganismNot specified

UniProt B9EI85

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain P； UniProt 15–24	Fragment：ACETYLATED H3 PEPTIDE, RESIDUES 15-24 Non-standard monomer：Yes (specific site not provided by mmCIF)	BROMODOMAIN TESTIS-SPECIFIC PROTEIN × 1 （Q91Y44）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；BRDT BD2 PROTEIN AT 25 MG/ML WAS MIXED WITH H3-ACK18 PEPTIDE IN A 1:5 MOLAR RATIO. CRYSTALLIZATION WAS BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 2.0 M AMMONIUM SULFATE, 2% PEG 400, 0.1 M HEPES PH 7.5	Resolution 2.10 Å R-free 0.255
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain Q； UniProt 15–24	Fragment：ACETYLATED H3 PEPTIDE, RESIDUES 15-24 Non-standard monomer：Yes (specific site not provided by mmCIF)	BROMODOMAIN TESTIS-SPECIFIC PROTEIN × 1 （Q91Y44）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；BRDT BD2 PROTEIN AT 25 MG/ML WAS MIXED WITH H3-ACK18 PEPTIDE IN A 1:5 MOLAR RATIO. CRYSTALLIZATION WAS BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 2.0 M AMMONIUM SULFATE, 2% PEG 400, 0.1 M HEPES PH 7.5	Resolution 2.10 Å R-free 0.255

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	B9EI85_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–10； UniProt 15–24 Author chain Q； PDBConstruct 1–10； UniProt 15–24

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	2wp1
Deposition date deposition_date	2009-08-02
Structure title title	Structure of Brdt bromodomain 2 bound to an acetylated histone H3 peptide
Keywords keywords	;TRANSCRIPTION PEPTIDE COMPLEX, TRANSCRIPTION REGULATION, ACETYLLYSINE BRDT, NUCLEUS, COILED COIL, CHROMOSOMAL PROTEIN, NUCLEOSOME, TRANSCRIPTION-PEPTIDE complex ;; TRANSCRIPTION/PEPTIDE
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	19.76 Å
Radius of gyration Rg (electron density) rg_electron	18.58 Å
Forward intensity I(0) i0	14420200.00
Molecular weight molecular_weight	28942.0 kDa
Excluded volume excluded_volume	36389 Å³
Envelope volume envelope_volume	42529 Å³
Hydration-shell volume shell_volume	18992 Å³
Envelope diameter envelope_diameter	64.9 Å
Shell Rg shell_rg	24.99 Å
Envelope Rg envelope_rg	19.04 Å
Shape Rg shape_rg	18.59 Å
Total Rg total_rg	19.53 Å
Total atoms total_atoms	2036
Residues n_residues	253
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	63.8 Å
Rg (real space) rg_real	19.65 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	1.4420e+07
I(0) uncertainty (real space) i0_real_error	1.6810e+05
Rg (reciprocal space) rg_reciprocal	19.67 Å
I(0) (reciprocal space) i0_reciprocal	14420000.0000
Solution quality estimate total_estimate	0.8867
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.190
Kurtosis Kurtosis kurtosis	-0.374
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4598000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.923

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	BROMODOMAIN TESTIS-SPECIFIC PROTEIN
Molecular weight formula_weight	14753.9 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	2247

QQQHKVLKTVKVTEQLKHCSEILKEMLAKKHLPYAWPFYNPVDADALGLHNYYDVVKNPMDLGTIKGKMDNQEYKDAYEFAADVRLMFMNCYKYNPPDHEVVAMARTLQDVFELHFAKIPDEPIES

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	HISTONE H3
Molecular weight formula_weight	1185.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

KAPRKQLATK

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	211

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2wp1A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	2wp1B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

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8. Citations (1)

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Unit-cell length a length_a	101.300 Å
Unit-cell length b length_b	101.300 Å
Unit-cell length c length_c	79.350 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	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.2550

fit	/app/data/saxs_computation/wp/2wp1/2wp1.fit
pddf	/app/data/pr_computation/wp/2wp1/2wp1.pr.out
profile	/app/data/saxs_computation/wp/2wp1/2wp1.dat

Structure of Brdt bromodomain 2 bound to an acetylated histone H3 peptide

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

BROMODOMAIN TESTIS-SPECIFIC PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

HISTONE H3

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)