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2wwu

Crystal structure of the catalytic domain of PHD finger protein 8

Method: X-RAY DIFFRACTION Dmax: 70.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHD FINGER PROTEIN 8

HOMO SAPIENS

UniProt Q9UPP1

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 115–483 Fragment：CATALYTIC DOMAIN, RESIDUES 115-483 SO4 SULFATE ION × 14 ACT ACETATE ION × 10 NI NICKEL (II) ION × 2 BGC beta-D-glucopyranose × 4 X-RAY DIFFRACTION X-ray crystallization conditions：1.5 M (NH4)2SO4, 0.1 M SODIUM ACETATE PH 4.25 Resolution 2.15 Å R-free 0.211

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 2WWU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3KV4 Structure of PHF8 in complex with histone H3 Deposited 2009-11-29 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 37–483（447 aa） Fragment：UNP Residues 37-483
Not recorded ZN ZINC ION × 2 FE2 FE (II) ION × 1 NI NICKEL (II) ION × 1 EDO 1,2-ETHANEDIOL × 13 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；25% (v/v) polyethylene glycol 3350, 0.2 M NaCl, and 0.1 M NaCitrate pH 5.6, VAPOR DIFFUSION, HANGING DROP
Resolution 2.19 Å R-free 0.255
4DO0 Crystal Structure of human PHF8 in complex with Daminozide Deposited 2012-02-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 115–483（369 aa）
Not recorded DZA DAMINOZIDE × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 12 EDO 1,2-ETHANEDIOL × 6 ACT ACETATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；277 K；0.1M acetate, 2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, temperature 277K
Resolution 2.55 Å R-free 0.265
7CMZ Crystal Structure of BRCT7/8 in Complex with the APS Motif of PHF8 Deposited 2020-07-29 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 842–863（22 aa）
Not recorded K POTASSIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；289 K；Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic
Resolution 1.70 Å R-free 0.215

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

View Construct and Data Evidence
UniProt name PHF8_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–371； UniProt 115–483

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2wwu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2wwu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2wwu
Deposition date deposition_date2009-10-29
Structure title titleCrystal structure of the catalytic domain of PHD finger protein 8
Keywords keywordsJMJC DOMAIN, EPIGENETICS, METAL-BINDING PROTEIN, HISTONE DEMETHYLASE, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.60 Å
Radius of gyration Rg (electron density) rg_electron21.26 Å
Forward intensity I(0) i030909400.00
Molecular weight molecular_weight42450.0 kDa
Excluded volume excluded_volume52934 ų
Envelope volume envelope_volume62292 ų
Hydration-shell volume shell_volume24354 ų
Envelope diameter envelope_diameter73.4 Å
Shell Rg shell_rg28.32 Å
Envelope Rg envelope_rg21.49 Å
Shape Rg shape_rg21.23 Å
Total Rg total_rg22.26 Å
Total atoms total_atoms2980
Residues n_residues363
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax70.5 Å
Rg (real space) rg_real22.52 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real3.0910e+07
I(0) uncertainty (real space) i0_real_error3.8670e+05
Rg (reciprocal space) rg_reciprocal22.54 Å
I(0) (reciprocal space) i0_reciprocal30910000.0000
Solution quality estimate total_estimate0.8063
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary27.8 Å
Skewness Skewness skewness0.264
Kurtosis Kurtosis kurtosis-0.338
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8583000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.830; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2wwua_
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.2 — Clavaminate synthase-like
Family Family familyb.82.2.14 — Jumonji domain / Histone demethylase core

CATH v4.4 (2 domains)

Domain ID domain_id2wwuA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily650 — Cupin
Domain ID domain_id2wwuA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily1360 —
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8. Citations (1)

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9. Files and Curves (10)