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- PDB-1hh8: The active N-terminal region of p67phox: Structure at 1.8 Angstro... -

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Basic information

Entry
Database: PDB / ID: 1hh8
TitleThe active N-terminal region of p67phox: Structure at 1.8 Angstrom resolution and biochemical characterizations of the A128V mutant implicated in chronic granulomatous disease
ComponentsNEUTROPHIL CYTOSOL FACTOR 2
KeywordsCELL CYCLE / PHAGOCYTE OXIDASE FACTOR / SH3 DOMAIN / TPR REPEAT CELL CYCLE
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
CITRATE ANION / Neutrophil cytosol factor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsGrizot, S. / Fieschi, F. / Dagher, M.-C. / Pebay-Peyroula, E.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The Active N-Terminal Region of P67Phox: Structure at 1.8 Angstrom Resolution and Biochemical Characterizations of the A128V Mutant Implicated in Chronic Granulomatous Disease
Authors: Grizot, S. / Fieschi, F. / Dagher, M.-C. / Pebay-Peyroula, E.
History
DepositionDec 21, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 20, 2017Group: Advisory / Database references / Category: pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / Item: _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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7082
Polymers24,5191
Non-polymers1891
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.670, 67.670, 50.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein NEUTROPHIL CYTOSOL FACTOR 2 / P67PHOX / NCF-2


Mass: 24518.551 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: NEUTROPHIL / Cellular location: CYTOPLASM / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19878
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 45 %
Description: PHASES AT 2.8 A WERE OBTAINED FROM A SAD DATA SET COLLECTED ON ID29 USING A SE-MET PROTEIN
Crystal growpH: 4.5
Details: 100 MM NA CITRATE PH 4.5, 17% PEG 2K MME, 10% GLYCEROL
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-6 mg/mlprotein1drop
217 %PEG2000 MME1reservoir
3100 mMsodium citrate1reservoir
410 %glycerol1reservoir
510 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorDate: Oct 15, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 23850 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 16.1 Å2 / Rsym value: 0.047 / Net I/σ(I): 12.4
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.198 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 95808 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.198

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
CCP4data scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 972845 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1213 5.1 %RANDOM
Rwork0.182 ---
obs0.182 23707 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.8284 Å2 / ksol: 0.370973 e/Å3
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20.09 Å20 Å2
2---1.09 Å20 Å2
3---2.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 13 160 1739
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.911.5
X-RAY DIFFRACTIONc_mcangle_it1.412
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 210 5.3 %
Rwork0.233 3726 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3FLC.PARFLC.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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