SAXSdb — 4ez4

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

Lysine-specific demethylase 6B

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1155–1293 Chain A； UniProt 1321–1641	Fragment：UNP residues 1155-1641	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.2；293 K；11% methanol, 6% MPD, 5% PEG 4K, 5% Glycerol, HEPES pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.99 Å R-free 0.250
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1155–1293 Chain B； UniProt 1321–1641	Fragment：UNP residues 1155-1641	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.2；293 K；11% methanol, 6% MPD, 5% PEG 4K, 5% Glycerol, HEPES pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.99 Å R-free 0.250

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 4EZ4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4EYU The free structure of the mouse C-terminal domain of KDM6B Deposited 2012-05-01	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1155–1293（139 aa） Fragment：UNP residues 1155-1641 Chain A 1321–1641（321 aa） Fragment：UNP residues 1155-1641	Not recorded	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；298 K；11% methanol, 6% MPD, 5% PEG 4K, 5% GLYCEROL, HEPES pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.268
4EYU The free structure of the mouse C-terminal domain of KDM6B Deposited 2012-05-01	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1155–1293（139 aa） Fragment：UNP residues 1155-1641 Chain B 1321–1641（321 aa） Fragment：UNP residues 1155-1641	Not recorded	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；298 K；11% methanol, 6% MPD, 5% PEG 4K, 5% GLYCEROL, HEPES pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.268
4EZH the crystal structure of KDM6B bound with H3K27me3 peptide Deposited 2012-05-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1155–1293（139 aa） Fragment：UNP residues 1155-1641 Chain A 1321–1641（321 aa） Fragment：UNP residues 1155-1641	Not recorded	NI NICKEL (II) ION × 1 ZN ZINC ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；293 K；11% methanol, 6% MPD, 5% PEG 4K, 5% Glycerol, HEPES 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.52 Å R-free 0.254
4EZH the crystal structure of KDM6B bound with H3K27me3 peptide Deposited 2012-05-02	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1155–1293（139 aa） Fragment：UNP residues 1155-1641 Chain B 1321–1641（321 aa） Fragment：UNP residues 1155-1641	Not recorded	NI NICKEL (II) ION × 1 ZN ZINC ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；293 K；11% methanol, 6% MPD, 5% PEG 4K, 5% Glycerol, HEPES 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.52 Å R-free 0.254
9NQU KDM6B-nucleosome structure stabilized by H3K27C-UNC8015 covalent conjugate Deposited 2025-03-13	Different construct Different mutation/modification 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 K 1130–1641（512 aa）	Not recorded	FE FE (III) ION × 1 ZN ZINC ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.16 Å

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KDM6B_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–139； UniProt 1155–1293 Author chain A； PDBConstruct 166–486； UniProt 1321–1641 Author chain B； PDBConstruct 1–139； UniProt 1155–1293 Author chain B； PDBConstruct 166–486； UniProt 1321–1641

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	4ez4
Deposition date deposition_date	2012-05-02
Structure title title	free KDM6B structure
Keywords keywords	mjd3/KDM6B, JmjC domain, histone demethylase, OXIDOREDUCTASE; OXIDOREDUCTASE
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	32.06 Å
Radius of gyration Rg (electron density) rg_electron	31.35 Å
Forward intensity I(0) i0	166933000.00
Molecular weight molecular_weight	102500.0 kDa
Excluded volume excluded_volume	127950 Å³
Envelope volume envelope_volume	161220 Å³
Hydration-shell volume shell_volume	42216 Å³
Envelope diameter envelope_diameter	108.0 Å
Shell Rg shell_rg	38.97 Å
Envelope Rg envelope_rg	31.23 Å
Shape Rg shape_rg	31.34 Å
Total Rg total_rg	32.00 Å
Total atoms total_atoms	7226
Residues n_residues	895
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	99.4 Å
Rg (real space) rg_real	31.96 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	1.6690e+08
I(0) uncertainty (real space) i0_real_error	2.4870e+06
Rg (reciprocal space) rg_reciprocal	32.01 Å
I(0) (reciprocal space) i0_reciprocal	166900000.0000
Solution quality estimate total_estimate	0.9060
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.6 Å
Skewness Skewness skewness	0.217
Kurtosis Kurtosis kurtosis	-0.514
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	50590000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.899

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Lysine-specific demethylase 6B
Molecular weight formula_weight	54886.0 kDa
EC 编号 ec_number	1.14.112
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	7268

ESYLSPAQSVKPKINTEEKLPREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEELEVLFQGPTKAARKSAPATGGGSSGSHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSENGSRNTYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAPASTSR

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 non-polymer

Description description	N-OXALYLGLYCINE
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4ez4A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	4ez4A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1370 —

Domain ID domain_id	4ez4A03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4ez4B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	4ez4B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1370 —

Domain ID domain_id	4ez4B03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	57.660 Å
Unit-cell length b length_b	123.707 Å
Unit-cell length c length_c	82.043 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.62 °
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	2.990 Å
Low-resolution limit resolution_low	49.730 Å
R factor r_factor	0.1930
R_work r_work	0.1900
R_free r_free	0.2500

fit	/app/data/saxs_computation/ez/4ez4/4ez4.fit
pddf	/app/data/pr_computation/ez/4ez4/4ez4.pr.out
profile	/app/data/saxs_computation/ez/4ez4/4ez4.dat

free KDM6B structure

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

Lysine-specific demethylase 6B

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