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- PDB-1wm5: Crystal structure of the N-terminal TPR domain (1-203) of p67phox -

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Basic information

Entry
Database: PDB / ID: 1wm5
TitleCrystal structure of the N-terminal TPR domain (1-203) of p67phox
ComponentsNeutrophil cytosol factor 2
KeywordsHormone/Growth Factor / Tetratricopeptide repeats / Hormone-Growth Factor COMPLEX
Function / homology
Function and homology information


superoxide-generating NADPH oxidase activator activity / superoxide-generating NAD(P)H oxidase activity / phagolysosome / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / ROS and RNS production in phagocytes / superoxide anion generation / superoxide metabolic process / Detoxification of Reactive Oxygen Species ...superoxide-generating NADPH oxidase activator activity / superoxide-generating NAD(P)H oxidase activity / phagolysosome / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / respiratory burst / ROS and RNS production in phagocytes / superoxide anion generation / superoxide metabolic process / Detoxification of Reactive Oxygen Species / RHO GTPases Activate NADPH Oxidases / RAC3 GTPase cycle / RAC2 GTPase cycle / cellular defense response / phagocytosis / RAC1 GTPase cycle / acrosomal vesicle / small GTPase binding / VEGFA-VEGFR2 Pathway / electron transfer activity / innate immune response / membrane / plasma membrane / cytosol
Similarity search - Function
Neutrophil cytosol factor 2, PB1 domain / Neutrophil cytosol factor 2 / Neutrophil cytosol factor 2, SH3 domain 1 / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. ...Neutrophil cytosol factor 2, PB1 domain / Neutrophil cytosol factor 2 / Neutrophil cytosol factor 2, SH3 domain 1 / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / SH3 domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Neutrophil cytosol factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsInagaki, F. / Suzuki, N.N.
CitationJournal: To be Published
Title: Crystal structure of the N-terminal TPR domain (1-203) of p67phox
Authors: Inagaki, F. / Suzuki, N.N.
History
DepositionJul 3, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Neutrophil cytosol factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4707
Polymers23,8941
Non-polymers5766
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.671, 121.671, 45.709
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Neutrophil cytosol factor 2 / NCF-2 / Neutrophil NADPH oxidase factor 2 / 67 kDa neutrophil oxidase factor / p67-phox / NOXA2


Mass: 23893.926 Da / Num. of mol.: 1 / Fragment: TPR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P19878
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: ammonium sulfate, HEPES, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.95→41.9 Å / Num. all: 17115 / Num. obs: 17115 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 8
Reflection shellResolution: 1.95→2.06 Å / Rmerge(I) obs: 0.189 / % possible all: 60.4

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E96

1e96


Resolution: 1.95→30.42 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1328861.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1684 10 %RANDOM
Rwork0.185 ---
all0.189 16903 --
obs0.189 16903 92.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.614 Å2 / ksol: 0.401592 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.13 Å2-1.23 Å20 Å2
2---5.13 Å20 Å2
3---10.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.95→30.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 30 172 1817
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it2.542
X-RAY DIFFRACTIONc_scangle_it3.72.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 179 9.6 %
Rwork0.252 1689 -
obs-1868 60.7 %
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

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