SAXSdb — 3pu3

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

PHD finger protein 2

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 60–451	Fragment：Jumonji domain (unp residues 60-451)	OGA N-OXALYLGLYCINE × 1 EDO 1,2-ETHANEDIOL × 22 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 1.95 Å R-free 0.294
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 60–451	Fragment：Jumonji domain (unp residues 60-451)	OGA N-OXALYLGLYCINE × 1 EDO 1,2-ETHANEDIOL × 21	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 1.95 Å R-free 0.294

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 3PU3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3KQI crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide Deposited 2009-11-17	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 A 1–70（70 aa） Fragment：PHD finger	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；2.0 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.78 Å R-free 0.218
3KQI crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide Deposited 2009-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–70（70 aa） Fragment：PHD finger	Not recorded	ZN ZINC ION × 4 GOL GLYCEROL × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；2.0 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.78 Å R-free 0.218
3PTR PHF2 Jumonji domain Deposited 2010-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	EDO 1,2-ETHANEDIOL × 19	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 1.95 Å R-free 0.229
3PU8 PHF2 Jumonji-NOG-Fe(II) complex Deposited 2010-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	OXY OXYGEN MOLECULE × 1 EDO 1,2-ETHANEDIOL × 6 OGA N-OXALYLGLYCINE × 1 CL CHLORIDE ION × 1 FE FE (III) ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 1.94 Å R-free 0.235
3PU8 PHF2 Jumonji-NOG-Fe(II) complex Deposited 2010-12-03	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	OXY OXYGEN MOLECULE × 1 EDO 1,2-ETHANEDIOL × 12 OGA N-OXALYLGLYCINE × 1 CL CHLORIDE ION × 1 FE FE (III) ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 1.94 Å R-free 0.235
3PUA PHF2 Jumonji-NOG-Ni(II) Deposited 2010-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	NI NICKEL (II) ION × 1 EDO 1,2-ETHANEDIOL × 11 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 1.89 Å R-free 0.210
3PUS PHF2 Jumonji-NOG-Ni(II) Deposited 2010-12-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	EDO 1,2-ETHANEDIOL × 5 CL CHLORIDE ION × 1 NI NICKEL (II) ION × 1 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 2.08 Å R-free 0.232
3PUS PHF2 Jumonji-NOG-Ni(II) Deposited 2010-12-06	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 60–451（392 aa） Fragment：Jumonji domain (unp residues 60-451)	Not recorded	EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1 NI NICKEL (II) ION × 1 OGA N-OXALYLGLYCINE × 1 OXY OXYGEN MOLECULE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION	Resolution 2.08 Å R-free 0.232
7M10 PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1 Deposited 2021-03-11	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 A 1–70（70 aa） Fragment：PHD domain	Not recorded	ZN ZINC ION × 2 FMT FORMIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；292 K；3.5M Sodium Formate,100mM TRIS pH 8.2	Resolution 1.15 Å R-free 0.165
8F8Y PHF2 (PHD+JMJ) in Complex with VRK1 N-Terminal Peptide Deposited 2022-11-22	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 A 1–451（451 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 3.06 Å R-free 0.249
8F8Y PHF2 (PHD+JMJ) in Complex with VRK1 N-Terminal Peptide Deposited 2022-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–451（451 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 10 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 3.06 Å R-free 0.249
8F8Z PHF2 (PHD+JMJ) in Complex with H3 Histone N-Terminal Peptide Deposited 2022-11-22	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 A 1–451（451 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 3.30 Å R-free 0.256
8F8Z PHF2 (PHD+JMJ) in Complex with H3 Histone N-Terminal Peptide Deposited 2022-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–451（451 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 10 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；292 K；2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 3.30 Å R-free 0.256

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PHF2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–392； UniProt 60–451 Author chain B； PDBConstruct 1–392； UniProt 60–451

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	3pu3
Deposition date deposition_date	2010-12-03
Structure title title	PHF2 Jumonji domain-NOG complex
Keywords keywords	alpha-ketoglutarate-Fe2+ dependent dioxygenases, Histone Tail BINDING PROTEIN, PROTEIN BINDING; PROTEIN BINDING
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	33.81 Å
Radius of gyration Rg (electron density) rg_electron	33.34 Å
Forward intensity I(0) i0	106564000.00
Molecular weight molecular_weight	83367.0 kDa
Excluded volume excluded_volume	104700 Å³
Envelope volume envelope_volume	132570 Å³
Hydration-shell volume shell_volume	34552 Å³
Envelope diameter envelope_diameter	124.2 Å
Shell Rg shell_rg	38.17 Å
Envelope Rg envelope_rg	33.50 Å
Shape Rg shape_rg	33.34 Å
Total Rg total_rg	33.73 Å
Total atoms total_atoms	5871
Residues n_residues	724
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	114.9 Å
Rg (real space) rg_real	34.01 Å
Rg uncertainty (real space) rg_real_error	1.08 Å
I(0) (real space) i0_real	1.0660e+08
I(0) uncertainty (real space) i0_real_error	1.9100e+06
Rg (reciprocal space) rg_reciprocal	33.89 Å
I(0) (reciprocal space) i0_reciprocal	106600000.0000
Solution quality estimate total_estimate	0.8190
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.3 Å
Skewness Skewness skewness	0.465
Kurtosis Kurtosis kurtosis	-0.443
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29870000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.746; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.702; Smooth: 0.704

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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	PHD finger protein 2
Molecular weight formula_weight	44715.2 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	6325

STLKKKRTWHKHGPGQAPDVKPVQNGSQLFIKELRSRTFPSAEDVVARVPGSQLTLGYMEEHGFTEPILVPKKDGLGLAVPAPTFYVSDVENYVGPERSVDVTDVTKQKDCKMKLKEFVDYYYSTNRKRVLNVTNLEFSDTRMSSFVEPPDIVKKLSWVENYWPDDALLAKPKVTKYCLICVKDSYTDFHIDSGGASAWYHVLKGEKTFYLIRPASANISLYERWRSASNHSEMFFADQVDKCYKCIVKQGQTLFIPSGWIYATLTPVDCLAFAGHFLHSLSVEMQMRAYEVERRLKLGSLTQFPNFETACWYMGKHLLEAFKGSHKSGKQLPPHLVQGAKILNGAFRSWTKKQALAEHEDELPEHFKPSQLIKDLAKEIRLSENASKAVRP

来源 Source

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

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	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	43

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	373

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3pu3a_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.14 — Jumonji domain / Histone demethylase core

Domain ID domain_id	d3pu3b_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.14 — Jumonji domain / Histone demethylase core

CATH v4.4 (4 domains)

Domain ID domain_id	3pu3A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	3pu3A02
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	1360 —

Domain ID domain_id	3pu3B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	650 — Cupin

Domain ID domain_id	3pu3B02
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	1360 —

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8. Citations (1)

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Unit-cell length a length_a	65.910 Å
Unit-cell length b length_b	96.335 Å
Unit-cell length c length_c	66.373 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	89.91 °
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	1.950 Å
Low-resolution limit resolution_low	31.180 Å
R factor r_factor	0.2285
R_work r_work	0.2261
R_free r_free	0.2937

fit	/app/data/saxs_computation/pu/3pu3/3pu3.fit
pddf	/app/data/pr_computation/pu/3pu3/3pu3.pr.out
profile	/app/data/saxs_computation/pu/3pu3/3pu3.dat

PHF2 Jumonji domain-NOG complex

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

PHD finger protein 2

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