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- PDB-1h6h: Structure of the PX domain from p40phox bound to phosphatidylinos... -

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Basic information

Entry
Database: PDB / ID: 1h6h
TitleStructure of the PX domain from p40phox bound to phosphatidylinositol 3-phosphate
ComponentsNEUTROPHIL CYTOSOL FACTOR 4
KeywordsPX DOMAIN
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 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PIB / Neutrophil cytosol factor 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsKarathanassis, D. / Bravo, J. / Pacold, M. / Perisic, O. / Williams, R.L.
Citation
Journal: Mol.Cell / Year: 2001
Title: The Crystal Structure of the Px Domain from P40Phox Bound to Phosphatidylinositol 3-Phosphate
Authors: Bravo, J. / Karathanassis, D. / Pacold, C.M. / Pacold, M.E. / Ellson, C.D. / Anderson, K.E. / Butler, J.G. / Lavenir, I. / Perisic, O. / Hawkins, P.T. / Stephens, L. / Williams, R.L.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: Solution Structure of the Px Domain, a Target of the SH3 Domain
Authors: Hiroaki, H. / Ago, T. / Ito, T. / Sumimoto, H. / Kohda, D.
History
DepositionJun 15, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUTROPHIL CYTOSOL FACTOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9593
Polymers16,3131
Non-polymers6462
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.760, 33.642, 76.430
Angle α, β, γ (deg.)90.00, 132.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 16312.643 Da / Num. of mol.: 1 / Fragment: PX DOMAIN RESIDUES 2-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: NEUTROPHIL / Plasmid: PQE / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q15080
#2: Chemical ChemComp-PIB / 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE / D-MYO-PHOSPHATIDYLINOSITOL 3-PHOSPHATED (+)-SN-1,2-DI-O-BUTANOYLGLYCERYL,3-O-PHOSPHO


Mass: 554.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H32O16P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.802 Å3/Da / Density % sol: 54.41 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop / Details: used hair seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.9 mg/mlprotein1drop
22 mMdi-C4-PtdIns(3)P1drop
310 %PEG60001reservoir
4100 mMHEPES1reservoir
5100 mM1reservoirNaCl
615 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2001 / Details: RH COATED SI MIRROR
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.7→56.4 Å / Num. obs: 18117 / % possible obs: 89.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 6.7
Reflection shellResolution: 1.7→1.77 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 4.2 / % possible all: 50.6
Reflection
*PLUS
Num. measured all: 55546
Reflection shell
*PLUS
% possible obs: 50.6 % / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 1.7→30.73 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1091987.27 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 921 5.1 %RANDOM
Rwork0.196 ---
obs0.196 18117 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.4807 Å2 / ksol: 0.370188 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å23.47 Å2
2---3.54 Å20 Å2
3---4.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.7→30.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 41 182 1373
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 76 4.5 %
Rwork0.237 1620 -
obs--50.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2I3P.PARI3P.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4GOL.PARGOL.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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