SAXSdb — 1o7k

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

NEUTROPHIL CYTOSOL FACTOR 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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–123 Chain B； UniProt 1–123 Chain C； UniProt 1–123	Fragment：PX DOMAIN, RESIDUES 1-123 Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；1 M AMMONIUM SULPHATE, 0.1M TRIS PH 8.5, 12% GLYCEROL	Resolution 2.00 Å R-free 0.254

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 1O7K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GD5 SOLUTION STRUCTURE OF THE PX DOMAIN FROM HUMAN P47PHOX NADPH OXIDASE Deposited 2000-09-14	Different construct Different mutation/modification Different oligomeric state 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 1–128（128 aa） Fragment：PX DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；293 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR sample composition 0.6mM PX domain U-15N,13C; 5mM Na-MES buffer; 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
1K4U Solution structure of the C-terminal SH3 domain of p67phox complexed with the C-terminal tail region of p47phox Deposited 2001-10-08	Different construct Different mutation/modification 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 P 359–390（32 aa） Fragment：TAIL PEPTIDE (RESIDUES 359-390)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.1；298 K；Ionic strength (raw mmCIF value) 100mM KCl；Pressure 1 NMR sample composition 0.7mM p67SH3(C) U-15N,13C; 0.77mM p47 tail peptide; 5mM MOPSO buffer; 30 mM d10-DTT; 100mM KCl \| 90% H2O, 10% D2O; 100% D2O NMR sample composition 0.5mM p47 tail peptide U-15N,13C; 0.55mM p67SH3(C); 5mM MOPSO buffer; 30mM d10-DTT; 100mM KCl \| 90% H2O, 10% D2O; 100% D2O	Resolution not provided
1KQ6 p47phox PX domain Deposited 2002-01-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–141（141 aa） Fragment：PX domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；PEG 550 DME, glycerol, ammonium sulfate, natrium citrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.18 Å R-free 0.185
1NG2 Structure of autoinhibited p47phox Deposited 2002-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 156–340（185 aa） Fragment：residues 156-340	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.233
1NG2 Structure of autoinhibited p47phox Deposited 2002-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 156–340（185 aa） Fragment：residues 156-340	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；PEG 3000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.70 Å R-free 0.233
1OV3 Structure of the p22phox-p47phox complex Deposited 2003-03-25	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 A 156–285（130 aa） Fragment：Residues 156-285 Chain B 156–285（130 aa） Fragment：Residues 156-285	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1 M Na-Citrate, 0.1 M Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.275
1OV3 Structure of the p22phox-p47phox complex Deposited 2003-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 156–285（130 aa） Fragment：Residues 156-285 Chain B 156–285（130 aa） Fragment：Residues 156-285	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1 M Na-Citrate, 0.1 M Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.275
1UEC Crystal structure of autoinhibited form of tandem SH3 domain of p47phox Deposited 2003-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 151–340（190 aa） Fragment：autoinhibited tandem SH3 domain, redidues 151-340	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；16% PEG 6000, 0.1M soduim citrate, 50mM sodium fluoride, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.82 Å R-free 0.236
1UEC Crystal structure of autoinhibited form of tandem SH3 domain of p47phox Deposited 2003-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 151–340（190 aa） Fragment：autoinhibited tandem SH3 domain, redidues 151-340	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；293 K；16% PEG 6000, 0.1M soduim citrate, 50mM sodium fluoride, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.82 Å R-free 0.236
1W70 SH3 domain of p40phox complexed with C-terminal polyProline region of p47phox Deposited 2004-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 360–372（13 aa） Fragment：POLYPROLINE MOTIF, RESIDUES 360-372	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；VAPOR DIFFUSION AT 20 DEGRE C AT 14MG/ML OF P40PHOX SH3 WITH A1/5 RATIO WITH POLYPROLINE PEPTIDE, 20 MM HEPES PH 7.5, 150 MM NACL MIXED WITH 100 MM NA-CITRATE/CITRIC ACID PH5, 2.4 M SA	Resolution 1.46 Å R-free 0.207
1W70 SH3 domain of p40phox complexed with C-terminal polyProline region of p47phox Deposited 2004-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 360–372（13 aa） Fragment：POLYPROLINE MOTIF, RESIDUES 360-372	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 TFA trifluoroacetic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；VAPOR DIFFUSION AT 20 DEGRE C AT 14MG/ML OF P40PHOX SH3 WITH A1/5 RATIO WITH POLYPROLINE PEPTIDE, 20 MM HEPES PH 7.5, 150 MM NACL MIXED WITH 100 MM NA-CITRATE/CITRIC ACID PH5, 2.4 M SA	Resolution 1.46 Å R-free 0.207
1WLP Solution Structure Of The P22Phox-P47Phox Complex Deposited 2004-06-29	Different construct Different mutation/modification 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 B 151–286（136 aa） Fragment：Tandem SH3 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
7YXW Structure of the p22phox A200G mutant in complex with p47phox peptide Deposited 2022-02-16	Different construct Different mutation/modification 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 156–285（130 aa）	Mutation：A200G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5, 1.2 M sodium citrate tribasic dihydrate, 1:1 protein:precipitant ratio	Resolution 2.50 Å R-free 0.269
8WEJ Structure of human phagocyte NADPH oxidase in the activated state Deposited 2023-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 1–286（286 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.79 Å

10 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NCF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–131； UniProt 1–123 Author chain B； PDBConstruct 9–131； UniProt 1–123 Author chain C； PDBConstruct 9–131； UniProt 1–123

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	1o7k
Deposition date deposition_date	2002-11-07
Structure title title	human p47 PX domain complex with sulphates
Keywords keywords	P47, NADPH OXIDASE, PX DOMAIN, PHOSPHOLIPID-BINDING, PHOSPHOINOSITIDE-BINDING, SH3 DOMAIN; SH3 DOMAIN
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	21.95 Å
Radius of gyration Rg (electron density) rg_electron	20.89 Å
Forward intensity I(0) i0	32901100.00
Molecular weight molecular_weight	44469.0 kDa
Excluded volume excluded_volume	55574 Å³
Envelope volume envelope_volume	66728 Å³
Hydration-shell volume shell_volume	25739 Å³
Envelope diameter envelope_diameter	66.3 Å
Shell Rg shell_rg	28.28 Å
Envelope Rg envelope_rg	20.95 Å
Shape Rg shape_rg	20.87 Å
Total Rg total_rg	21.87 Å
Total atoms total_atoms	3098
Residues n_residues	354
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	65.3 Å
Rg (real space) rg_real	21.74 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	3.2900e+07
I(0) uncertainty (real space) i0_real_error	3.5960e+05
Rg (reciprocal space) rg_reciprocal	21.78 Å
I(0) (reciprocal space) i0_reciprocal	32900000.0000
Solution quality estimate total_estimate	0.9040
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.2 Å
Skewness Skewness skewness	0.026
Kurtosis Kurtosis kurtosis	-0.528
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9766000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	NEUTROPHIL CYTOSOL FACTOR 1
Molecular weight formula_weight	15879.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3309

MAHHHHHHMGDTFIRHIALLGFEKRFVPSQHYVYMFLVKWQDLSEKVVYRRFTEIYEFHKTLKEMFPIEAGAINPENRIIPHLPAPKWFDGQRAAENRQGTLTEYCSTLMSLPTKISRCPHLLDFFKVRPD

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	194

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1o7ka1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.189 — PX domain
Superfamily Superfamily superfamily	d.189.1 — PX domain
Family Family family	d.189.1.1 — PX domain

Domain ID domain_id	d1o7ka2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1o7kb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.189 — PX domain
Superfamily Superfamily superfamily	d.189.1 — PX domain
Family Family family	d.189.1.1 — PX domain

Domain ID domain_id	d1o7kc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.189 — PX domain
Superfamily Superfamily superfamily	d.189.1 — PX domain
Family Family family	d.189.1.1 — PX domain

CATH v4.4 (3 domains)

Domain ID domain_id	1o7kA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1520 — PX Domain
Homologous superfamily homologous superfamily	10 — Phox-like domain

Domain ID domain_id	1o7kB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1520 — PX Domain
Homologous superfamily homologous superfamily	10 — Phox-like domain

Domain ID domain_id	1o7kC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1520 — PX Domain
Homologous superfamily homologous superfamily	10 — Phox-like domain

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8. Citations (1)

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Unit-cell length a length_a	74.233 Å
Unit-cell length b length_b	92.175 Å
Unit-cell length c length_c	144.010 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	77.000 Å
R factor r_factor	0.2230
R_work r_work	0.2100
R_free r_free	0.2540

fit	/app/data/saxs_computation/o7/1o7k/1o7k.fit
pddf	/app/data/pr_computation/o7/1o7k/1o7k.pr.out
profile	/app/data/saxs_computation/o7/1o7k/1o7k.dat

human p47 PX domain complex with sulphates

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

NEUTROPHIL CYTOSOL FACTOR 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

Diffraction experiment Diffraction