SAXSdb — 1z9q

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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 168–233	Fragment：SH3 domain	No other associated polymer	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

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 1Z9Q	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 ligand/ion Different experimental method 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 method 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 method 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 method 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 method 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 experimental method 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 experimental method 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 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 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 oligomeric state Different ligand/ion Different experimental method 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
2DYB The crystal structure of human p40(phox) Deposited 2006-09-08	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 1–339（339 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	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
2DYB The crystal structure of human p40(phox) Deposited 2006-09-08	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–339（339 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	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

5 other PDB entries and 11 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 14–79； UniProt 168–233

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	1z9q
Deposition date deposition_date	2005-04-04
Structure title title	Solution structure of SH3 domain of p40phox
Keywords keywords	Oxidoreductase Activator; Oxidoreductase Activator
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	11.79 Å
Radius of gyration Rg (electron density) rg_electron	11.46 Å
Forward intensity I(0) i0	269392000.00
Molecular weight molecular_weight	147990.0 kDa
Excluded volume excluded_volume	188840 Å³
Envelope volume envelope_volume	15188 Å³
Hydration-shell volume shell_volume	10091 Å³
Envelope diameter envelope_diameter	42.9 Å
Shell Rg shell_rg	18.48 Å
Envelope Rg envelope_rg	13.84 Å
Shape Rg shape_rg	11.39 Å
Total Rg total_rg	11.90 Å
Total atoms total_atoms	21040
Residues n_residues	1320
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	40.3 Å
Rg (real space) rg_real	11.77 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	2.6940e+08
I(0) uncertainty (real space) i0_real_error	3.0230e+06
Rg (reciprocal space) rg_reciprocal	11.78 Å
I(0) (reciprocal space) i0_reciprocal	269400000.0000
Solution quality estimate total_estimate	0.7768
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.8 Å
Skewness Skewness skewness	0.250
Kurtosis Kurtosis kurtosis	-0.191
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	67690.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.700; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1z9qa_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	1z9qA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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8. Citations (1)

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Description description	Neutrophil cytosol factor 4
Molecular weight formula_weight	9136.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	21040

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

fit	/app/data/saxs_computation/z9/1z9q/1z9q.fit
pddf	/app/data/pr_computation/z9/1z9q/1z9q.pr.out
profile	/app/data/saxs_computation/z9/1z9q/1z9q.dat

Solution structure of SH3 domain of p40phox

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)