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5xfn

Structure of the N-terminal domains of PHF1

Method: X-RAY DIFFRACTION Dmax: 78.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHD finger protein 1

Homo sapiens

UniProt O43189

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 25–340 Fragment：UNP residues 25-340 ZN ZINC ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Tris-pH 8.0, 10% PEG 3350, 22% ethylene glycerol Resolution 1.90 Å R-free 0.218

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 5XFN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2E5P Solution structure of the TUDOR domain of PHD finger protein 1 (PHF1 protein) Deposited 2006-12-22 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–83（55 aa） Fragment：TUDOR domain, residues 8-62
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O | 90% H2O/10% D2O
Resolution not provided
2M0O The solution structure of human PHF1 in complex with H3K36me3 Deposited 2012-10-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 6–83（78 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.3-0.5 mM [U-100% 13C; U-100% 15N] PHF1 tudor, 0.6-1.0 mM H3K36me3 peptide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
4HCZ PHF1 Tudor in complex with H3K36me3 Deposited 2012-10-01 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 28–85（58 aa） Fragment：Tudor domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；0.1 M HEPES pH 7.5, 20% PEG 10000, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Resolution 1.85 Å R-free 0.244
4HCZ PHF1 Tudor in complex with H3K36me3 Deposited 2012-10-01 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 28–85（58 aa） Fragment：Tudor domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；0.1 M HEPES pH 7.5, 20% PEG 10000, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Resolution 1.85 Å R-free 0.244
5XFO Structure of the N-terminal domains of PHF1 Deposited 2017-04-11 Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–340（316 aa） Fragment：UNP residues 25-340
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Tris-pH 8.0, 10% PEG 3350, 22% ethylene glycerol
Resolution 1.90 Å R-free 0.227
5XFP Binary complex of PHF1 and a double stranded DNA Deposited 2017-04-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–360（336 aa） Fragment：UNP residues 25-360
Not recorded ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Tris-pH 8.5, 25% PEG 3350, 0.2M Li2SO4, 10mM MgCl2
Resolution 2.30 Å R-free 0.244
5XFP Binary complex of PHF1 and a double stranded DNA Deposited 2017-04-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 25–360（336 aa） Fragment：UNP residues 25-360
Not recorded ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Tris-pH 8.5, 25% PEG 3350, 0.2M Li2SO4, 10mM MgCl2
Resolution 2.30 Å R-free 0.244
5XFP Binary complex of PHF1 and a double stranded DNA Deposited 2017-04-11 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 25–360（336 aa） Fragment：UNP residues 25-360
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Tris-pH 8.5, 25% PEG 3350, 0.2M Li2SO4, 10mM MgCl2
Resolution 2.30 Å R-free 0.244
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain AA 28–87（60 aa）
Chain AC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 10 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain JA 28–87（60 aa）
Chain JC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 11 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain KA 28–87（60 aa）
Chain KC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 12 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain LA 28–87（60 aa）
Chain LC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 13 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain MA 28–87（60 aa）
Chain MC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 14 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain NA 28–87（60 aa）
Chain NC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 15 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain OA 28–87（60 aa）
Chain OC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain BA 28–87（60 aa）
Chain BC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain CA 28–87（60 aa）
Chain CC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain DA 28–87（60 aa）
Chain DC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain EA 28–87（60 aa）
Chain EC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain FA 28–87（60 aa）
Chain FC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain GA 28–87（60 aa）
Chain GC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain HA 28–87（60 aa）
Chain HC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAT complex structure of PHF1 Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain IA 28–87（60 aa）
Chain IC 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.4M ammonium phosphate dibasic and 0.1M HEPES pH7.0
Resolution 1.80 Å R-free 0.268
6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 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 28–87（60 aa）
Not recorded SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
Resolution 1.70 Å R-free 0.241
6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 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 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
Resolution 1.70 Å R-free 0.241
6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
Resolution 1.70 Å R-free 0.241
6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 28–87（60 aa）
Not recorded UNX UNKNOWN LIGAND × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
Resolution 1.70 Å R-free 0.241
7LKY Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641 Deposited 2021-02-03 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 28–87（60 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277.15 K；0.01 M ZnCl2, 0.1 M MES pH 6.0 and 20% PEG 6000
Resolution 1.85 Å R-free 0.281
7LKY Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641 Deposited 2021-02-03 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 28–87（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277.15 K；0.01 M ZnCl2, 0.1 M MES pH 6.0 and 20% PEG 6000
Resolution 1.85 Å R-free 0.281
7LKY Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641 Deposited 2021-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 28–87（60 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277.15 K；0.01 M ZnCl2, 0.1 M MES pH 6.0 and 20% PEG 6000
Resolution 1.85 Å R-free 0.281
7LKY Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641 Deposited 2021-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 28–87（60 aa）
Not recorded ZN ZINC ION × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277.15 K；0.01 M ZnCl2, 0.1 M MES pH 6.0 and 20% PEG 6000
Resolution 1.85 Å R-free 0.281
7LKY Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641 Deposited 2021-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 28–87（60 aa）
Not recorded ZN ZINC ION × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277.15 K；0.01 M ZnCl2, 0.1 M MES pH 6.0 and 20% PEG 6000
Resolution 1.85 Å R-free 0.281
7LKY Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641 Deposited 2021-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 28–87（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277.15 K；0.01 M ZnCl2, 0.1 M MES pH 6.0 and 20% PEG 6000
Resolution 1.85 Å R-free 0.281
7LKY Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641 Deposited 2021-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 28–87（60 aa）
Not recorded DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277.15 K；0.01 M ZnCl2, 0.1 M MES pH 6.0 and 20% PEG 6000
Resolution 1.85 Å R-free 0.281
7LKY Crystal Structure of PHF1 Tudor domain in complex with a peptidomimetic ligand UNC6641 Deposited 2021-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 28–87（60 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277.15 K；0.01 M ZnCl2, 0.1 M MES pH 6.0 and 20% PEG 6000
Resolution 1.85 Å R-free 0.281

8 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PHF1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–316； UniProt 25–340

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 5xfn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5xfn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5xfn
Deposition date deposition_date2017-04-11
Structure title titleStructure of the N-terminal domains of PHF1
Keywords keywordsPHF1, PCL1, PRC2, TRANSCRIPTION; TRANSCRIPTION
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_guinier22.90 Å
Radius of gyration Rg (electron density) rg_electron22.23 Å
Forward intensity I(0) i021483200.00
Molecular weight molecular_weight34474.0 kDa
Excluded volume excluded_volume42835 ų
Envelope volume envelope_volume52499 ų
Hydration-shell volume shell_volume20604 ų
Envelope diameter envelope_diameter77.7 Å
Shell Rg shell_rg28.33 Å
Envelope Rg envelope_rg22.53 Å
Shape Rg shape_rg22.25 Å
Total Rg total_rg22.98 Å
Total atoms total_atoms2401
Residues n_residues301
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 dmax78.9 Å
Rg (real space) rg_real22.99 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real2.1480e+07
I(0) uncertainty (real space) i0_real_error3.1290e+05
Rg (reciprocal space) rg_reciprocal22.97 Å
I(0) (reciprocal space) i0_reciprocal21480000.0000
Solution quality estimate total_estimate0.8615
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.3 Å
Skewness Skewness skewness0.487
Kurtosis Kurtosis kurtosis-0.168
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3993000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.781; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.911; Smooth: 0.957
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id5xfnA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
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8. Citations (1)

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9. Files and Curves (10)