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- PDB-2dyb: The crystal structure of human p40(phox) -

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Basic information

Entry
Database: PDB / ID: 2dyb
TitleThe crystal structure of human p40(phox)
ComponentsNeutrophil cytosol factor 4
KeywordsOXIDOREDUCTASE / p40(phox) / NADPH oxidase
Function / homology
Function and homology information


superoxide-generating NADPH oxidase activator activity / phagolysosome / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / phosphatidylinositol-3-phosphate binding / ROS and RNS production in phagocytes / superoxide anion generation / Detoxification of Reactive Oxygen Species / RHO GTPases Activate NADPH Oxidases ...superoxide-generating NADPH oxidase activator activity / phagolysosome / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / phosphatidylinositol-3-phosphate binding / ROS and RNS production in phagocytes / superoxide anion generation / Detoxification of Reactive Oxygen Species / RHO GTPases Activate NADPH Oxidases / RAC2 GTPase cycle / RAC3 GTPase cycle / phagocytosis / RAC1 GTPase cycle / VEGFA-VEGFR2 Pathway / endosome membrane / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Neutrophil cytosol factor P40 / Neutrophil cytosol factor P40, PB1 domain / Neutrophil cytosol factor 4, PX domain / Neutrophil cytosol factor P40, SH3 domain / Phox-like domain / PX Domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain ...Neutrophil cytosol factor P40 / Neutrophil cytosol factor P40, PB1 domain / Neutrophil cytosol factor 4, PX domain / Neutrophil cytosol factor P40, SH3 domain / Phox-like domain / PX Domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / SH3 Domains / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SH3 domain / SH3 type barrels. / Src homology 3 domains / Ubiquitin-like (UB roll) / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Neutrophil cytosol factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsHonbou, K.
CitationJournal: Embo J. / Year: 2007
Title: Full-length p40phox structure suggests a basis for regulation mechanism of its membrane binding.
Authors: Honbou, K. / Minakami, R. / Yuzawa, S. / Takeya, R. / Suzuki, N.N. / Kamakura, S. / Sumimoto, H. / Inagaki, F.
History
DepositionSep 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neutrophil cytosol factor 4
B: Neutrophil cytosol factor 4


Theoretical massNumber of molelcules
Total (without water)78,6622
Polymers78,6622
Non-polymers00
Water00
1
A: Neutrophil cytosol factor 4


Theoretical massNumber of molelcules
Total (without water)39,3311
Polymers39,3311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil cytosol factor 4


Theoretical massNumber of molelcules
Total (without water)39,3311
Polymers39,3311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.273, 189.813, 79.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Neutrophil cytosol factor 4 / NCF-4 / Neutrophil NADPH oxidase factor 4 / p40-phox / p40phox


Mass: 39330.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pProEX HTb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q15080

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5% PEG 20000, 200mM Bis-tris-HCl, 10mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 22612 / Num. obs: 22612 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6H, 1W6X, and 1OEY

1h6h

1w6x

1oey


Resolution: 3.15→40.8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 231491.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1912 10 %RANDOM
Rwork0.263 ---
obs0.263 19197 97.7 %-
all-21840 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.0898 Å2 / ksol: 0.303304 e/Å3
Displacement parametersBiso mean: 82.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å20 Å2
2---22.61 Å20 Å2
3---21.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3.15→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4252 0 0 0 4252
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.21
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.15→3.35 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 350 11.5 %
Rwork0.353 2684 -
obs--93.8 %
Xplor fileSerial no: 1 / Param file: protein2.param / Topol file: protein2.top

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