SAXSdb — 5b1l

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

Histone H4

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–DNA Heteromer Protein × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts	Chain B； UniProt 1–103 Chain F； UniProt 1–103	Not recorded	Histone H3t × 2 Histone H2A type 1 × 2 （P22752） Histone H2B type 3-A × 2 （Q9D2U9） DNA (146-MER) × 2 CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.35 Å R-free 0.243

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 5B1L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1F66 2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z Deposited 2000-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain B 1–102（102 aa） Chain F 1–102（102 aa）	Not recorded	MN MANGANESE (II) ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.60 Å R-free 0.249
2WP2 Structure of Brdt bromodomain BD1 bound to a diacetylated histone H4 peptide. Deposited 2009-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 2–21（20 aa） Fragment：RESIDUES 2-21	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 2–21（20 aa） Fragment：RESIDUES 2-21	Non-standard monomer：Yes (specific site not provided by mmCIF)	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
4AU7 The structure of the Suv4-20h2 ternary complex with histone H4 Deposited 2012-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 18–26（9 aa） Fragment：RESIDUES 18-26	Non-standard monomer：Yes (specific site not provided by mmCIF)	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；PROTEIN WAS CRYSTALLIZED FROM 9% PEG 3350, 0.1 M HEPES PH 6.5	Resolution 2.07 Å R-free 0.240
4DOW Structure of mouse ORC1 BAH domain bound to H4K20me2 Deposited 2012-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 15–26（12 aa） Fragment：UNP residues 15-26	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.2 M sodium bromide, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.95 Å R-free 0.257
4DOW Structure of mouse ORC1 BAH domain bound to H4K20me2 Deposited 2012-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 15–26（12 aa） Fragment：UNP residues 15-26	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.2 M sodium bromide, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.95 Å R-free 0.257
5B1M The mouse nucleosome structure containing H3.1 Deposited 2015-12-08	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain B 1–103（103 aa） Chain F 1–103（103 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.34 Å R-free 0.259
5XM0 The mouse nucleosome structure containing H2A, H2B type3-A, H3.3, and H4 Deposited 2017-05-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain B 1–103（103 aa） Chain F 1–103（103 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.87 Å R-free 0.255
5XM1 The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4 Deposited 2017-05-12	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain B 1–103（103 aa） Chain F 1–103（103 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 3.45 Å R-free 0.254
7DBH The mouse nucleosome structure containing H3mm18 Deposited 2020-10-20	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain B 1–103（103 aa） Chain F 1–103（103 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7VBM The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv Deposited 2021-08-31	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain B 1–103（103 aa） Chain F 1–103（103 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
8PKI Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5 Deposited 2023-06-26	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric	Chain B 1–103（103 aa） Chain F 1–103（103 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.58 Å

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H4_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–106； UniProt 1–103 Author chain F； PDBConstruct 4–106； UniProt 1–103

Histone H2A type 1

Mus musculus

UniProt P22752

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–DNA Heteromer Protein × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts	Chain C； UniProt 1–130 Chain G； UniProt 1–130	Not recorded	Histone H3t × 2 Histone H4 × 2 （P62806） Histone H2B type 3-A × 2 （Q9D2U9） DNA (146-MER) × 2 CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.35 Å R-free 0.243

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 5B1L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5B1M The mouse nucleosome structure containing H3.1 Deposited 2015-12-08	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–130（130 aa） Chain G 1–130（130 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.34 Å R-free 0.259

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

View Construct and Data Evidence

UniProt name	H2A1_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–133； UniProt 1–130 Author chain G； PDBConstruct 4–133； UniProt 1–130

Histone H2B type 3-A

Mus musculus

UniProt Q9D2U9

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–DNA Heteromer Protein × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts	Chain D； UniProt 1–126 Chain H； UniProt 1–126	Not recorded	Histone H3t × 2 Histone H4 × 2 （P62806） Histone H2A type 1 × 2 （P22752） DNA (146-MER) × 2 CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.35 Å R-free 0.243

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 5B1L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1U35 Crystal structure of the nucleosome core particle containing the histone domain of macroH2A Deposited 2004-07-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–126（126 aa） Chain H 1–126（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；potassium chloride, manganese chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 3.00 Å R-free 0.260
2F8N 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes Deposited 2005-12-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–125（125 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；34 to 37.5mM KCl and 40-45mM MnCl2, 5mM Potassium Cacodylate, Sample concentration: 8-12 mg/ml, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.90 Å R-free 0.269
5B1M The mouse nucleosome structure containing H3.1 Deposited 2015-12-08	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–126（126 aa） Chain H 1–126（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.34 Å R-free 0.259
5XM0 The mouse nucleosome structure containing H2A, H2B type3-A, H3.3, and H4 Deposited 2017-05-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–126（126 aa） Chain H 1–126（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 2.87 Å R-free 0.255
5XM1 The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4 Deposited 2017-05-12	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–126（126 aa） Chain H 1–126（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride	Resolution 3.45 Å R-free 0.254
7DBH The mouse nucleosome structure containing H3mm18 Deposited 2020-10-20	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–126（126 aa） Chain H 1–126（126 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7VBM The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv Deposited 2021-08-31	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–126（126 aa） Chain H 1–126（126 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H2B3A_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 4–129； UniProt 1–126 Author chain H； PDBConstruct 4–129； UniProt 1–126

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	5b1l
Deposition date deposition_date	2015-12-08
Structure title title	The mouse nucleosome structure containing H3t
Keywords keywords	chromatin, spermatogenesis, histone-fold, STRUCTURAL PROTEIN-DNA complex; STRUCTURAL PROTEIN/DNA
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	39.69 Å
Radius of gyration Rg (electron density) rg_electron	36.93 Å
Forward intensity I(0) i0	827834000.00
Molecular weight molecular_weight	175620.0 kDa
Excluded volume excluded_volume	194630 Å³
Envelope volume envelope_volume	283100 Å³
Hydration-shell volume shell_volume	62106 Å³
Envelope diameter envelope_diameter	118.0 Å
Shell Rg shell_rg	44.71 Å
Envelope Rg envelope_rg	36.41 Å
Shape Rg shape_rg	36.75 Å
Total Rg total_rg	37.68 Å
Total atoms total_atoms	11939
Residues n_residues	1043
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	114.1 Å
Rg (real space) rg_real	39.41 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	8.2780e+08
I(0) uncertainty (real space) i0_real_error	1.3120e+07
Rg (reciprocal space) rg_reciprocal	39.59 Å
I(0) (reciprocal space) i0_reciprocal	828000000.0000
Solution quality estimate total_estimate	0.8883
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	45.6 Å
Skewness Skewness skewness	0.072
Kurtosis Kurtosis kurtosis	-0.706
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	60690000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.989; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.587

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Histone H3t
Molecular weight formula_weight	15744.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	12164

GSHMARTKQTARKSTGGKAPRKQLATKVARKSAPATGGVKKPHRYHPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACESYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Histone H4
Molecular weight formula_weight	11676.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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 3 Entity 3 polymer

Description description	Histone H2A type 1
Molecular weight formula_weight	14447.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

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 BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Histone H2B type 3-A
Molecular weight formula_weight	14307.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H

GSHMPEPSRSTPAPKKGSKKAITKAQKKDGKKRKRGRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIASEASRLAHYNKRSTITSREVQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

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 BL21(DE3)

Entity 5 Entity 5 polymer

Description description	DNA (146-MER)
Molecular weight formula_weight	45053.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,J

ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli DH5[alpha]

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	225

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d5b1lb_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d5b1lc_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d5b1ld_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d5b1lf_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d5b1lg_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d5b1lh_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

CATH v4.4 (8 domains)

Domain ID domain_id	5b1lA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5b1lB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5b1lC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5b1lD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5b1lE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5b1lF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5b1lG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5b1lH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

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8. Citations (1)

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Unit-cell length a length_a	98.968 Å
Unit-cell length b length_b	107.425 Å
Unit-cell length c length_c	167.332 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	8

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

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	41.833 Å
R factor r_factor	0.1993
R_work r_work	0.1969
R_free r_free	0.2429

fit	/app/data/saxs_computation/b1/5b1l/5b1l.fit
pddf	/app/data/pr_computation/b1/5b1l/5b1l.pr.out
profile	/app/data/saxs_computation/b1/5b1l/5b1l.dat

The mouse nucleosome structure containing H3t

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

Histone H4

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2A type 1

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2B type 3-A

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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)