SAXSdb — 2f5k

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–90	Fragment：chromo domain	No other associated polymer	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–90	Fragment：chromo domain	No other associated polymer	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–90	Fragment：chromo domain	No other associated polymer	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–90	Fragment：chromo domain	No other associated polymer	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
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 1–90	Fragment：chromo domain	No other associated polymer	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
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 1–90	Fragment：chromo domain	No other associated polymer	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

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 2F5K	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 mutation/modification Different oligomeric state 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 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
2F5J Crystal structure of MRG domain from human MRG15 Deposited 2005-11-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 190–362（173 aa） Fragment：MRG domain Chain B 190–362（173 aa） Fragment：MRG domain	Not recorded	No recorded non-water small molecule	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
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 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 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 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 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 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 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 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MO4L1_HUMAN
Isoform	Q9UBU8-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–102； UniProt 1–90 Author chain B； PDBConstruct 13–102； UniProt 1–90 Author chain C； PDBConstruct 13–102； UniProt 1–90 Author chain D； PDBConstruct 13–102； UniProt 1–90 Author chain E； PDBConstruct 13–102； UniProt 1–90 Author chain F； PDBConstruct 13–102； UniProt 1–90

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	2f5k
Deposition date deposition_date	2005-11-26
Structure title title	Crystal structure of the chromo domain of human MRG15
Keywords keywords	beta barrel, 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	30.24 Å
Radius of gyration Rg (electron density) rg_electron	29.61 Å
Forward intensity I(0) i0	53085200.00
Molecular weight molecular_weight	58121.0 kDa
Excluded volume excluded_volume	73295 Å³
Envelope volume envelope_volume	97698 Å³
Hydration-shell volume shell_volume	28471 Å³
Envelope diameter envelope_diameter	105.8 Å
Shell Rg shell_rg	35.69 Å
Envelope Rg envelope_rg	29.20 Å
Shape Rg shape_rg	29.61 Å
Total Rg total_rg	30.25 Å
Total atoms total_atoms	4114
Residues n_residues	483
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	101.3 Å
Rg (real space) rg_real	30.35 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	5.3090e+07
I(0) uncertainty (real space) i0_real_error	9.2590e+05
Rg (reciprocal space) rg_reciprocal	30.31 Å
I(0) (reciprocal space) i0_reciprocal	53080000.0000
Solution quality estimate total_estimate	0.8512
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.2 Å
Skewness Skewness skewness	0.365
Kurtosis Kurtosis kurtosis	-0.627
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11430000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.871; Smooth: 0.931

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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) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2f5ka1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.3 — Chromo barrel domain

Domain ID domain_id	d2f5kb_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.3 — Chromo barrel domain

Domain ID domain_id	d2f5kc_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.3 — Chromo barrel domain

Domain ID domain_id	d2f5kd_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.3 — Chromo barrel domain

Domain ID domain_id	d2f5ke_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.3 — Chromo barrel domain

Domain ID domain_id	d2f5kf_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.3 — Chromo barrel domain

CATH v4.4 (6 domains)

Domain ID domain_id	2f5kA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2f5kB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2f5kC01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2f5kD01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2f5kE01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2f5kF01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

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8. Citations (1)

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Unit-cell length a length_a	109.480 Å
Unit-cell length b length_b	80.313 Å
Unit-cell length c length_c	81.285 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	123.91 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2270
R_work r_work	0.2245
R_free r_free	0.2727

Description description	Mortality factor 4-like protein 1
Molecular weight formula_weight	12251.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	4571

Crystal structure of the chromo domain of 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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 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	457

fit	/app/data/saxs_computation/f5/2f5k/2f5k.fit
pddf	/app/data/pr_computation/f5/2f5k/2f5k.pr.out
profile	/app/data/saxs_computation/f5/2f5k/2f5k.dat