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- PDB-1ng2: Structure of autoinhibited p47phox -

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Basic information

Entry
Database: PDB / ID: 1ng2
TitleStructure of autoinhibited p47phox
ComponentsNeutrophil cytosolic factor 1
KeywordsOxidoreductase activator / p47phox / autoinhibited / SH3 domain / NADPH oxidase
Function / homology
Function and homology information


reactive oxygen species biosynthetic process / regulation of respiratory burst involved in inflammatory response / superoxide-generating NADPH oxidase activator activity / phagolysosome / superoxide-generating NAD(P)H oxidase activity / positive regulation of epidermal growth factor-activated receptor activity / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / cellular response to testosterone stimulus ...reactive oxygen species biosynthetic process / regulation of respiratory burst involved in inflammatory response / superoxide-generating NADPH oxidase activator activity / phagolysosome / superoxide-generating NAD(P)H oxidase activity / positive regulation of epidermal growth factor-activated receptor activity / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / cellular response to testosterone stimulus / ROS and RNS production in phagocytes / phosphatidylinositol-3,4-bisphosphate binding / superoxide anion generation / protein targeting to membrane / positive regulation of p38MAPK cascade / superoxide metabolic process / Detoxification of Reactive Oxygen Species / RHO GTPases Activate NADPH Oxidases / RAC2 GTPase cycle / RAC3 GTPase cycle / cellular defense response / RAC1 GTPase cycle / cellular response to cadmium ion / phosphatidylinositol binding / cellular response to glucose stimulus / positive regulation of JNK cascade / cytoplasmic side of plasma membrane / VEGFA-VEGFR2 Pathway / SH3 domain binding / cellular response to reactive oxygen species / electron transfer activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / innate immune response / neuronal cell body / dendrite / positive regulation of DNA-templated transcription / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Neutrophil cytosol factor 1 / Neutrophil cytosol factor 1, C-terminal / Neutrophil cytosol factor 1, PBR/AIR / Neutrophil cytosol factor 1, PX domain / Neutrophil cytosol factor 1, first SH3 domain / Neutrophil cytosol factor 1, second SH3 domain / NADPH oxidase subunit p47Phox, C terminal domain / Neutrophil cytosol factor 1, PBR/AIR / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. ...Neutrophil cytosol factor 1 / Neutrophil cytosol factor 1, C-terminal / Neutrophil cytosol factor 1, PBR/AIR / Neutrophil cytosol factor 1, PX domain / Neutrophil cytosol factor 1, first SH3 domain / Neutrophil cytosol factor 1, second SH3 domain / NADPH oxidase subunit p47Phox, C terminal domain / Neutrophil cytosol factor 1, PBR/AIR / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Neutrophil cytosol factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsGroemping, Y. / Lapouge, K. / Smerdon, S.J. / Rittinger, K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Molecular basis of phosphorylation-induced activation of the NADPH oxidase
Authors: Groemping, Y. / Lapouge, K. / Smerdon, S.J. / Rittinger, K.
History
DepositionDec 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300Biomolecule: The biologically active unit is generated using amino acid 201-332 from the molecule ...Biomolecule: The biologically active unit is generated using amino acid 201-332 from the molecule in the asymmetric unit and amino acids 157-199 from a symmetry related molecule, which can be generated by the following operations: y, x,-z (rotation) and 0,0,1 (translation)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neutrophil cytosolic factor 1


Theoretical massNumber of molelcules
Total (without water)22,0631
Polymers22,0631
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Neutrophil cytosolic factor 1

A: Neutrophil cytosolic factor 1


Theoretical massNumber of molelcules
Total (without water)44,1252
Polymers44,1252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5760 Å2
ΔGint-42 kcal/mol
Surface area19030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.986, 99.986, 44.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biologically active unit is generated using amino acid 201-332 from the molecule in the asymmetric unit and amino acids 157-199 from a symmetry related molecule, which can be generated by the following operations: y, x,-z (rotation) and 0,0,1 (translation).

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Components

#1: Protein Neutrophil cytosolic factor 1 / NCF-1 / Neutrophil NADPH oxidase factor 1 / 47 kDa neutrophil oxidase factor / p47-phox / NCF-47K / ...NCF-1 / Neutrophil NADPH oxidase factor 1 / 47 kDa neutrophil oxidase factor / p47-phox / NCF-47K / 47 kDa autosomal chronic granulomatous disease protein


Mass: 22062.742 Da / Num. of mol.: 1 / Fragment: residues 156-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCF1 / Plasmid: pGEX 6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P14598
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 3000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120-35 mg/mlprotein1drop
220 mMHEPES1droppH7.0
3100 mM1dropNaCl
42 mMdithiothreitol1drop
512 %PEG30001reservoir
6sodium citrate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978, 0.9798, 0.9793, 0.95
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2002 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.97981
30.97931
40.951
ReflectionResolution: 1.7→20 Å / Num. all: 25526 / Num. obs: 25449 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.5
Reflection shellResolution: 1.701→1.78 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3117 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 20 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.225 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1291 5.1 %RANDOM
Rwork0.206 ---
all0.208 25526 --
obs0.208 25449 99.7 %-
Displacement parametersBiso mean: 22.157 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.71 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 0 150 1564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211447
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9411958
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7473175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06415267
X-RAY DIFFRACTIONr_chiral_restr0.1150.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021118
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.3565
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.5176
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.390
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.522
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9731.5877
X-RAY DIFFRACTIONr_mcangle_it1.75821413
X-RAY DIFFRACTIONr_scbond_it2.4693570
X-RAY DIFFRACTIONr_scangle_it4.0754.5545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.289 85
Rwork0.263 1691
obs-1691
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

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