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- PDB-1w6x: SH3 domain of p40phox, component of the NADPH oxidase -

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Basic information

Entry
Database: PDB / ID: 1w6x
TitleSH3 domain of p40phox, component of the NADPH oxidase
ComponentsNEUTROPHIL CYTOSOL FACTOR 4
KeywordsSH3 DOMAIN / NADPH OXIDASE / P40PHOX / PHAGOCYTE
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 / RAC3 GTPase cycle / RAC2 GTPase cycle / phagocytosis / RAC1 GTPase cycle / VEGFA-VEGFR2 Pathway / endosome membrane / membrane / plasma membrane / cytosol / cytoplasm
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 / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. ...Neutrophil cytosol factor P40 / Neutrophil cytosol factor P40, PB1 domain / Neutrophil cytosol factor 4, PX domain / Neutrophil cytosol factor P40, SH3 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 / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Neutrophil cytosol factor 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMassenet, C. / Chenavas, S. / Cohen-Addad, C. / Dagher, M.-C. / Brandolin, G. / Pebay-Peyroula, E. / Fieschi, F.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Effects of P47Phox C-Terminus Phosphorylation on Binding Interactions with P40Phox and P67Phox: Structural and Functional Comparison of P40Phox P67Phox SH3 Domains
Authors: Massenet, C. / Chenavas, S. / Cohen-Addad, C. / Dagher, M.-C. / Brandolin, G. / Pebay-Peyroula, E. / Fieschi, F.
History
DepositionAug 24, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references / Category: citation / Item: _citation.page_last
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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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)13,5822
Polymers13,5822
Non-polymers00
Water1,09961
1
A: NEUTROPHIL CYTOSOL FACTOR 4


Theoretical massNumber of molelcules
Total (without water)6,7911
Polymers6,7911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NEUTROPHIL CYTOSOL FACTOR 4


Theoretical massNumber of molelcules
Total (without water)6,7911
Polymers6,7911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.160, 45.160, 35.060
Angle α, β, γ (deg.)90.00, 111.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NEUTROPHIL CYTOSOL FACTOR 4 / NCF-4 / NEUTROPHIL NADPH OXIDASE FACTOR 4 / P40PHOX / P40-PHOX


Mass: 6791.013 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, RESIDUES 174-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: NEUTROPHILE / Plasmid: PIVEX2.4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15080
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE STRUCTURE CORRESPONDS ONLY TO THE SH3 DOMAIN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.52 %
Description: THE STARTING MODEL CONSISTED OF A SUPERPOSITION OF 8 SH3 STRUCTURES 1SEM, 1SHG, 1ABQ, 1FYN, 1I0C,1B07, 1BB9, 1BU1 USING MAIN CHAIN ATOMS
Crystal growTemperature: 287 K / Method: vapor diffusion
Details: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: NONIUS / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 6876 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 3.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.4 / % possible all: 90

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 356 5.1 %RANDOM
Rwork0.2476 ---
obs0.2476 6871 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.9964 Å2 / ksol: 0.3542 e/Å3
Displacement parametersBiso mean: 32.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.417 Å20 Å211.028 Å2
2--4.579 Å20 Å2
3----4.162 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 0 61 943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006833
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_deg1.30239
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.37
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7771
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: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.438 45 6.36 %
Rwork0.3511 607 -
obs--92.1 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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