SAXSdb — 2dyb

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

Neutrophil cytosol factor 4

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 1–339	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；5% PEG 20000, 200mM Bis-tris-HCl, 10mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.302
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–339	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；5% PEG 20000, 200mM Bis-tris-HCl, 10mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.15 Å R-free 0.302

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 2DYB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H6H Structure of the PX domain from p40phox bound to phosphatidylinositol 3-phosphate Deposited 2001-06-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–144（143 aa） Fragment：PX DOMAIN RESIDUES 2-144	Not recorded	PIB 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.50	Resolution 1.70 Å R-free 0.232
1OEY Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 237–339（103 aa） Fragment：PB1 DOMAIN, RESIDUES 237-339	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；18% PEG 3350, 17% PEG 400, 4.8% ISOPROPYL ALCOHOL, 0.1 M CAPSO PH 9.0	Resolution 2.00 Å R-free 0.252
1OEY Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 237–339（103 aa） Fragment：PB1 DOMAIN, RESIDUES 237-339	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；18% PEG 3350, 17% PEG 400, 4.8% ISOPROPYL ALCOHOL, 0.1 M CAPSO PH 9.0	Resolution 2.00 Å R-free 0.252
1OEY Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 237–339（103 aa） Fragment：PB1 DOMAIN, RESIDUES 237-339	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；18% PEG 3350, 17% PEG 400, 4.8% ISOPROPYL ALCOHOL, 0.1 M CAPSO PH 9.0	Resolution 2.00 Å R-free 0.252
1OEY Heterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 237–339（103 aa） Fragment：PB1 DOMAIN, RESIDUES 237-339	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；18% PEG 3350, 17% PEG 400, 4.8% ISOPROPYL ALCOHOL, 0.1 M CAPSO PH 9.0	Resolution 2.00 Å R-free 0.252
1W6X SH3 domain of p40phox, component of the NADPH oxidase Deposited 2004-08-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 174–228（55 aa） Fragment：SH3 DOMAIN, RESIDUES 174-228	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；287 K；VAPOR DIFFUSION AT 14 DEGRE C, PROTEIN AT 14 MG/ML, 20 MM HEPES PH 7.5, 150 MM NACL MIXED WITH 40% PEG2K MME, 100 MM AS 200 MM NA AC PH 4.6.	Resolution 2.00 Å R-free 0.250
1W6X SH3 domain of p40phox, component of the NADPH oxidase Deposited 2004-08-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 174–228（55 aa） Fragment：SH3 DOMAIN, RESIDUES 174-228	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；287 K；VAPOR DIFFUSION AT 14 DEGRE C, PROTEIN AT 14 MG/ML, 20 MM HEPES PH 7.5, 150 MM NACL MIXED WITH 40% PEG2K MME, 100 MM AS 200 MM NA AC PH 4.6.	Resolution 2.00 Å R-free 0.250
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 A 174–228（55 aa） Fragment：SH3 DOMAIN, RESIDUES 174-228	Not recorded	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 B 174–228（55 aa） Fragment：SH3 DOMAIN, RESIDUES 174-228	Not recorded	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
1Z9Q Solution structure of SH3 domain of p40phox Deposited 2005-04-04	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 168–233（66 aa） Fragment：SH3 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 150mM NaCl；Pressure ambient NMR sample composition 0.5mM p40phoxSH3 U-13C, 15N; 50mM NaPi pH7.0; 150mM NaCl \| 90% H2O/10% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	NCF4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–341； UniProt 1–339 Author chain B； PDBConstruct 3–341； UniProt 1–339

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	2dyb
Deposition date deposition_date	2006-09-08
Structure title title	The crystal structure of human p40(phox)
Keywords keywords	p40(phox), NADPH oxidase, OXIDOREDUCTASE; OXIDOREDUCTASE
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	30.98 Å
Radius of gyration Rg (electron density) rg_electron	30.39 Å
Forward intensity I(0) i0	58620700.00
Molecular weight molecular_weight	60093.0 kDa
Excluded volume excluded_volume	75095 Å³
Envelope volume envelope_volume	104480 Å³
Hydration-shell volume shell_volume	30333 Å³
Envelope diameter envelope_diameter	106.9 Å
Shell Rg shell_rg	35.27 Å
Envelope Rg envelope_rg	30.39 Å
Shape Rg shape_rg	30.43 Å
Total Rg total_rg	30.76 Å
Total atoms total_atoms	4252
Residues n_residues	569
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	102.7 Å
Rg (real space) rg_real	31.06 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	5.8620e+07
I(0) uncertainty (real space) i0_real_error	1.0020e+06
Rg (reciprocal space) rg_reciprocal	31.03 Å
I(0) (reciprocal space) i0_reciprocal	58620000.0000
Solution quality estimate total_estimate	0.8818
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.3 Å
Skewness Skewness skewness	0.400
Kurtosis Kurtosis kurtosis	-0.232
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6630000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.868

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2dybA01
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	2dybA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	2dybA03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2dybB01
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	2dybB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	2dybB03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	146.273 Å
Unit-cell length b length_b	189.813 Å
Unit-cell length c length_c	79.883 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.150 Å
Low-resolution limit resolution_low	40.800 Å
R factor r_factor	0.2630
R_work r_work	0.2630
R_free r_free	0.3020

Description description	Neutrophil cytosol factor 4
Molecular weight formula_weight	39330.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4252

The crystal structure of human p40(phox)

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

Neutrophil cytosol factor 4

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/dy/2dyb/2dyb.fit
pddf	/app/data/pr_computation/dy/2dyb/2dyb.pr.out
profile	/app/data/saxs_computation/dy/2dyb/2dyb.dat