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- PDB-1uec: Crystal structure of autoinhibited form of tandem SH3 domain of p... -

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Basic information

Entry
Database: PDB / ID: 1uec
TitleCrystal structure of autoinhibited form of tandem SH3 domain of p47phox
ComponentsNeutrophil cytosol factor 1
KeywordsSIGNALING PROTEIN / NADPH oxidase / p47phox / phagocyte / SH3 domain / autoinhibition
Function / homology
Function and homology information


regulation of respiratory burst involved in inflammatory response / superoxide-generating NADPH oxidase activator activity / reactive oxygen species biosynthetic process / 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 ...regulation of respiratory burst involved in inflammatory response / superoxide-generating NADPH oxidase activator activity / reactive oxygen species biosynthetic process / 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 / VEGFA-VEGFR2 Pathway / SH3 domain binding / cytoplasmic side of plasma membrane / 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 / cytosol / cytoplasm
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. ...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: 1.82 Å
AuthorsYuzawa, S. / Suzuki, N.N. / Fujioka, Y. / Ogura, K. / Sumimoto, H. / Inagaki, F.
CitationJournal: Genes Cells / Year: 2004
Title: A molecular mechanism for autoinhibition of the tandem SH3 domains of p47phox, the regulatory subunit of the phagocyte NADPH oxidase
Authors: Yuzawa, S. / Suzuki, N.N. / Fujioka, Y. / Ogura, K. / Sumimoto, H. / Inagaki, F.
History
DepositionMay 11, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neutrophil cytosol factor 1


Theoretical massNumber of molelcules
Total (without water)22,0211
Polymers22,0211
Non-polymers00
Water2,774154
1


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

A: Neutrophil cytosol factor 1


Theoretical massNumber of molelcules
Total (without water)44,0412
Polymers44,0412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
Buried area5670 Å2
ΔGint-44 kcal/mol
Surface area18980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.217, 100.217, 44.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Neutrophil cytosol factor 1 / p47phox


Mass: 22020.729 Da / Num. of mol.: 1 / Fragment: autoinhibited tandem SH3 domain, redidues 151-340
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(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14598
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.58 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 16% PEG 6000, 0.1M soduim citrate, 50mM sodium fluoride, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Yuzawa, S., (2003) Acta Crystallogr., D59, 1479. / PH range low: 5.6 / PH range high: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125-35 mg/mlprotein1drop
250 mMsodium fluoride1drop
3100 mMsodium citrate1reservoirpH5.4-5.6
416-18 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Dec 9, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.82→300 Å / Num. all: 21103 / Num. obs: 21103 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.6
Reflection shellResolution: 1.82→1.86 Å / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 3.4 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 300 Å / Num. measured all: 124911 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MAD / Resolution: 1.82→40.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1681677.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2024 9.9 %RANDOM
Rwork0.213 ---
obs0.213 20491 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.9418 Å2 / ksol: 0.376146 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.33 Å20 Å20 Å2
2--4.33 Å20 Å2
3----8.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.82→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 0 154 1548
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_scangle_it3.422.5
LS refinement shellResolution: 1.82→1.93 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 319 10.2 %
Rwork0.257 2809 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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