SAXSdb — 7d86

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

PHD finger protein 14

Danio rerio

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 278–487	Fragment：PHF14-PZP	ZN ZINC ION × 5 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.2 M Magnesium chloride, 0.1 M Bis-Tris, 25 % v/v PEG 3350	Resolution 1.84 Å R-free 0.225

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 7D86	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7D87 Crystal Structure of zebrafish PHF14-PZP in complex with H3(1-25) Deposited 2020-10-07	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 278–487（210 aa） Fragment：PHF14-PZP	Not recorded	ZN ZINC ION × 5 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；0.1 M Carboxylic acids,0.1 M Buffer System 2, 37.50% % v/v MPD_P1K_P3350 (morpheus).	Resolution 2.11 Å R-free 0.204
7D8A Crystal Structure of H3(1-13)/PHF14-PZP fusion protein Deposited 2020-10-07	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 278–487（210 aa） Fragment：PHF14-PZP	Not recorded	ZN ZINC ION × 5 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Hepes pH 7.5, 18% PEG4000, 12% isopropanol .	Resolution 2.00 Å R-free 0.212

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A286Y9D1_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–211； UniProt 278–487

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	7d86
Deposition date deposition_date	2020-10-07
Structure title title	Crystal Structure of zebrafishPHF14-PZP
Keywords keywords	PHF14-PZP, 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	17.08 Å
Radius of gyration Rg (electron density) rg_electron	15.93 Å
Forward intensity I(0) i0	9417580.00
Molecular weight molecular_weight	20993.0 kDa
Excluded volume excluded_volume	25501 Å³
Envelope volume envelope_volume	30201 Å³
Hydration-shell volume shell_volume	15726 Å³
Envelope diameter envelope_diameter	53.6 Å
Shell Rg shell_rg	22.03 Å
Envelope Rg envelope_rg	16.26 Å
Shape Rg shape_rg	15.96 Å
Total Rg total_rg	16.84 Å
Total atoms total_atoms	1443
Residues n_residues	185
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	53.1 Å
Rg (real space) rg_real	16.95 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	9.4180e+06
I(0) uncertainty (real space) i0_real_error	1.0570e+05
Rg (reciprocal space) rg_reciprocal	16.97 Å
I(0) (reciprocal space) i0_reciprocal	9418000.0000
Solution quality estimate total_estimate	0.7538
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.086
Kurtosis Kurtosis kurtosis	-0.436
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1168000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 0.379; Positv: 1.000; Valcen: 0.985; Smooth: 0.979

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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 14
Molecular weight formula_weight	23349.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1535

SSSQRMEHILICCVCLGDNSEDADEIIQCDNCGVTVHEGCYGVDGESDSIMSSASENSTEPWFCDACKNGVSPSCELCPSQDGIFKETDAGRWVHVVCALYVPGVAFGDIDKLRPVTLTEMNYSKYGAKECSLCEDTRFARTGVCISCDAGMCRSFFHVTCAQREGLLSEAAAEEDIADPFFAYCKQHADRFDRKWKRKNYLALQSYCKVS

来源 Source

来源生物 organism	Danio rerio
通用名 common_name	Zebrafish
NCBI Class编号 ncbi_taxonomy_id	7955
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 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	92

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8. Citations (1)

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Unit-cell length a length_a	42.193 Å
Unit-cell length b length_b	41.907 Å
Unit-cell length c length_c	52.878 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.95 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.840 Å
Low-resolution limit resolution_low	41.680 Å
R factor r_factor	0.1793
R_work r_work	0.1744
R_free r_free	0.2246

fit	/app/data/saxs_computation/d8/7d86/7d86.fit
pddf	/app/data/pr_computation/d8/7d86/7d86.pr.out
profile	/app/data/saxs_computation/d8/7d86/7d86.dat

Crystal Structure of zebrafishPHF14-PZP

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

PHD finger protein 14

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