SAXSdb — 2f5j

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

Mortality factor 4-like protein 1

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 190–362 Chain B； UniProt 190–362	Fragment：MRG domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；20% PEG 4000, 0.1M HEPES, 5% iso-propanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 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 2F5J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2AQL Crystal Structure of the MRG15 MRG domain Deposited 2005-08-18	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 190–362（173 aa） Chain B 190–362（173 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；PEG 10000, cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.273
2EFI Solution structure of the chromo domain of Mortality factor 4-like protein 1 from human Deposited 2007-02-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–93（93 aa） Fragment：Chromo domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.13mM Chromo domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2F5K Crystal structure of the chromo domain of human MRG15 Deposited 2005-11-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–90（90 aa） Fragment：chromo domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273
2F5K Crystal structure of the chromo domain of human MRG15 Deposited 2005-11-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–90（90 aa） Fragment：chromo domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273
2F5K Crystal structure of the chromo domain of human MRG15 Deposited 2005-11-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–90（90 aa） Fragment：chromo domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273
2F5K Crystal structure of the chromo domain of human MRG15 Deposited 2005-11-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–90（90 aa） Fragment：chromo domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273
2F5K Crystal structure of the chromo domain of human MRG15 Deposited 2005-11-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–90（90 aa） Fragment：chromo domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273
2F5K Crystal structure of the chromo domain of human MRG15 Deposited 2005-11-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–90（90 aa） Fragment：chromo domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；14% PEG 3350, 0.2M potassium nitrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.273
2LKM Structural Basis for Molecular Interactions Involving MRG Domains: Implications in Chromatin Biology Deposited 2011-10-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 194–362（169 aa） Fragment：UNP residues 194-362	Mutation：K201R	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N] protein_1, 0.9 mM protein_2, 50 mM sodium phosphate, 10 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N] protein_1, 0.9 mM protein_2, 50 mM potassium chloride, 100 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 100% D2O \| 100% D2O NMR sample composition 0.9 mM protein_1, 0.9 mM [U-100% 13C; U-100% 15N] protein_2, 50 mM sodium phosphate, 10 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM protein_1, 0.9 mM [U-100% 13C; U-100% 15N] protein_2, 50 mM sodium phosphate, 100 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 100% D2O \| 100% D2O	Resolution not provided
2N1D Solution structure of the MRG15-MRGBP complex Deposited 2015-03-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 194–362（169 aa） Fragment：UNP residues 194-362	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.9；308 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] protein 1, 0.8 mM protein 2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] protein 1, 0.8 mM protein 2, 100% D2O \| 100% D2O NMR sample composition 0.9 mM protein 1, 0.9 mM [U-100% 13C; U-100% 15N] protein 2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM protein 1, 0.9 mM [U-100% 13C; U-100% 15N] protein 2, 100% D2O \| 100% D2O	Resolution not provided
6INE Crystal Structure of human ASH1L-MRG15 complex Deposited 2018-10-25	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 B 190–362（173 aa）	Not recorded	ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris-HCl pH 8.5, 20 % PEG 6000, 0.2 M Trimethylamine-N-oxide	Resolution 2.60 Å R-free 0.237
7S4A MRG15 complex with PALB2 peptide Deposited 2021-09-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 152–323（172 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；Ammonium sulfate, Tris HCl	Resolution 2.69 Å R-free 0.297
7S4A MRG15 complex with PALB2 peptide Deposited 2021-09-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 152–323（172 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；Ammonium sulfate, Tris HCl	Resolution 2.69 Å R-free 0.297
8BPA Cryo-EM structure of the human SIN3B histone deacetylase complex at 3.7 Angstrom Deposited 2022-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–362（362 aa）	Not recorded	ZN ZINC ION × 5 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8C60 Cryo-EM structure of the human SIN3B full-length complex at 3.4 Angstrom resolution Deposited 2023-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–362（362 aa）	Not recorded	ZN ZINC ION × 5 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

9 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MO4L1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–171； UniProt 190–362 Author chain B； PDBConstruct 1–171； UniProt 190–362

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	2f5j
Deposition date deposition_date	2005-11-26
Structure title title	Crystal structure of MRG domain from human MRG15
Keywords keywords	MRG fold, mainly a-helix, GENE REGULATION; GENE REGULATION
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	22.04 Å
Radius of gyration Rg (electron density) rg_electron	20.79 Å
Forward intensity I(0) i0	20004600.00
Molecular weight molecular_weight	36655.0 kDa
Excluded volume excluded_volume	47005 Å³
Envelope volume envelope_volume	55522 Å³
Hydration-shell volume shell_volume	22143 Å³
Envelope diameter envelope_diameter	72.0 Å
Shell Rg shell_rg	27.30 Å
Envelope Rg envelope_rg	20.97 Å
Shape Rg shape_rg	20.80 Å
Total Rg total_rg	21.68 Å
Total atoms total_atoms	2598
Residues n_residues	316
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	69.4 Å
Rg (real space) rg_real	21.93 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	2.0000e+07
I(0) uncertainty (real space) i0_real_error	2.5670e+05
Rg (reciprocal space) rg_reciprocal	21.95 Å
I(0) (reciprocal space) i0_reciprocal	20000000.0000
Solution quality estimate total_estimate	0.8256
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.9 Å
Skewness Skewness skewness	0.186
Kurtosis Kurtosis kurtosis	-0.537
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5529000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2f5jA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily	30 — MRG domain

Domain ID domain_id	2f5jB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily	30 — MRG domain

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8. Citations (1)

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Unit-cell length a length_a	111.151 Å
Unit-cell length b length_b	111.151 Å
Unit-cell length c length_c	86.991 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	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2065
R_work r_work	0.2046
R_free r_free	0.2432

Description description	Mortality factor 4-like protein 1
Molecular weight formula_weight	21143.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2836

Crystal structure of MRG domain from human MRG15

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

Mortality factor 4-like protein 1

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 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)

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 BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	238

fit	/app/data/saxs_computation/f5/2f5j/2f5j.fit
pddf	/app/data/pr_computation/f5/2f5j/2f5j.pr.out
profile	/app/data/saxs_computation/f5/2f5j/2f5j.dat