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- PDB-1o7k: human p47 PX domain complex with sulphates -

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Basic information

Entry
Database: PDB / ID: 1o7k
Titlehuman p47 PX domain complex with sulphates
ComponentsNEUTROPHIL CYTOSOL FACTOR 1
KeywordsSH3 DOMAIN / P47 / NADPH OXIDASE / PX DOMAIN / PHOSPHOLIPID-BINDING / PHOSPHOINOSITIDE-BINDING
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-like domain / PX Domain ...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-like domain / PX 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
Neutrophil cytosol factor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKarathanassis, D. / Bravo, J. / Perisic, O. / Pacold, C.M. / Williams, R.L.
CitationJournal: Embo J. / Year: 2002
Title: Binding of the Px Domain of P47Phox to Phosphatidylinositol 3.4-Bisphosphate and Phosphatidic Acid is Masked by an Intramolecular Interaction
Authors: Karathanassis, D. / Stahelin, R.V. / Bravo, J. / Perisic, O. / Pacold, C.M. / Cho, W. / Williams, R.L.
History
DepositionNov 7, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2002Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUTROPHIL CYTOSOL FACTOR 1
B: NEUTROPHIL CYTOSOL FACTOR 1
C: NEUTROPHIL CYTOSOL FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,31110
Polymers47,6393
Non-polymers6727
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.233, 92.175, 144.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11C-2040-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.61845, 0.467982, 0.631279), (-0.438825, -0.460737, 0.771462), (0.651884, -0.754131, -0.079581)3.611, 40.499, -8.841
2given(0.683484, -0.405776, 0.606791), (0.388947, -0.500989, -0.77313), (0.617714, 0.764431, -0.184593)-16.106, 26.834, 30.749

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Components

#1: Protein NEUTROPHIL CYTOSOL FACTOR 1 / NCF-1 / NEUTROPHIL NADPH OXIDASE FACTOR 1 / P47-PHOX / 47 KDA NEUTROPHIL OXIDASE FACTOR / NCF-47K / ...NCF-1 / NEUTROPHIL NADPH OXIDASE FACTOR 1 / P47-PHOX / 47 KDA NEUTROPHIL OXIDASE FACTOR / NCF-47K / 47 KDA AUTOSOMAL CHRONIC GRANULOMATOUS DISEASE PROTEIN


Mass: 15879.608 Da / Num. of mol.: 3 / Fragment: PX DOMAIN, RESIDUES 1-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Cell: NEUTROPHIL / Plasmid: PJL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P14598
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Compound detailsNCF2, NCF1, AND A MEMBRANE BOUND CYTOCHROME B558 ARE REQUIRED FOR ACTIVATION OF THE LATENT NADPH ...NCF2, NCF1, AND A MEMBRANE BOUND CYTOCHROME B558 ARE REQUIRED FOR ACTIVATION OF THE LATENT NADPH OXIDASE (NECESSARY FOR SUPEROXIDE PRODUCTION).
Sequence detailsMAHHHHHH N-TERMINAL AFFINITY TAG

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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: 2.9 Å3/Da / Density % sol: 52.5 %
Crystal growpH: 8.5
Details: 1 M AMMONIUM SULPHATE, 0.1M TRIS PH 8.5, 12% GLYCEROL
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / Details: used hair seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.0 Mammonium sulfate1reservoir
20.1 MTris1reservoirpH8.5
312 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.021409, 1.021248
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 28, 2001 / Details: BENT MIRROR
RadiationMonochromator: SI(311) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0214091
21.0212481
ReflectionResolution: 2→77 Å / Num. obs: 168658 / % possible obs: 93.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.92
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 1.7 / % possible all: 74.1
Reflection
*PLUS
Lowest resolution: 77 Å / Num. obs: 24307 / % possible obs: 93.6 % / Num. measured all: 83922 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 74.1 % / Mean I/σ(I) obs: 1.5

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
SHARPphasing
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 2→77 Å / SU B: 4.92 / SU ML: 0.1291 / Cross valid method: THROUGHOUT / ESU R: 0.1921 / ESU R Free: 0.1751
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1494 5 %RANDOM
Rwork0.21 ---
obs0.223 29890 93.7 %-
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2→77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 35 194 3292
Refinement
*PLUS
Lowest resolution: 38.9 Å / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg25
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.21 Å / Rfactor Rfree: 0.28 / Num. reflection Rfree: 225 / Rfactor Rwork: 0.254 / Num. reflection Rwork: 4313 / Total num. of bins used: 8

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