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- PDB-1oey: Heterodimer of p40phox and p67phox PB1 domains from human NADPH o... -

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Basic information

Entry
Database: PDB / ID: 1oey
TitleHeterodimer of p40phox and p67phox PB1 domains from human NADPH oxidase
Components
  • NEUTROPHIL CYTOSOL FACTOR 2
  • NEUTROPHIL CYTOSOL FACTOR 4
KeywordsIMMUNE SYSTEM / PB1 HETERODIMER-COMPLEX / NADPH OXIDASE / PB1 DOMAIN / HETERODIMERIZATION
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 / phosphatidylinositol-3-phosphate binding / ROS and RNS production in phagocytes / superoxide anion generation / superoxide metabolic process ...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 / phosphatidylinositol-3-phosphate binding / 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 / endosome membrane / innate immune response / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Neutrophil cytosol factor P40 / Neutrophil cytosol factor P40, PB1 domain / Neutrophil cytosol factor 2, PB1 domain / Neutrophil cytosol factor 2 / Neutrophil cytosol factor 4, PX domain / Neutrophil cytosol factor P40, SH3 domain / Neutrophil cytosol factor 2, SH3 domain 1 / PB1 domain / PB1 domain / PB1 domain profile. ...Neutrophil cytosol factor P40 / Neutrophil cytosol factor P40, PB1 domain / Neutrophil cytosol factor 2, PB1 domain / Neutrophil cytosol factor 2 / Neutrophil cytosol factor 4, PX domain / Neutrophil cytosol factor P40, SH3 domain / Neutrophil cytosol factor 2, SH3 domain 1 / 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 / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Tetratricopeptide repeat / SH3 domain / Src homology 3 domains / Ubiquitin-like (UB roll) / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Neutrophil cytosol factor 2 / Neutrophil cytosol factor 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsWilson, M.I. / Gill, D.J. / Perisic, O. / Quinn, M.T. / Williams, R.L.
CitationJournal: Mol.Cell / Year: 2003
Title: Pb1 Domain-Mediated Heterodimerization in Nadph Oxidase and Signaling Complexes of Atypical Protein Kinase C with Par6 and P62
Authors: Wilson, M.I. / Gill, D.J. / Perisic, O. / Quinn, M.T. / Williams, R.L.
History
DepositionApr 2, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Advisory / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUTROPHIL CYTOSOL FACTOR 2
B: NEUTROPHIL CYTOSOL FACTOR 2
C: NEUTROPHIL CYTOSOL FACTOR 2
D: NEUTROPHIL CYTOSOL FACTOR 2
J: NEUTROPHIL CYTOSOL FACTOR 4
K: NEUTROPHIL CYTOSOL FACTOR 4
L: NEUTROPHIL CYTOSOL FACTOR 4
M: NEUTROPHIL CYTOSOL FACTOR 4


Theoretical massNumber of molelcules
Total (without water)91,1568
Polymers91,1568
Non-polymers00
Water6,179343
1
A: NEUTROPHIL CYTOSOL FACTOR 2
J: NEUTROPHIL CYTOSOL FACTOR 4


Theoretical massNumber of molelcules
Total (without water)22,7892
Polymers22,7892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NEUTROPHIL CYTOSOL FACTOR 2
K: NEUTROPHIL CYTOSOL FACTOR 4


Theoretical massNumber of molelcules
Total (without water)22,7892
Polymers22,7892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: NEUTROPHIL CYTOSOL FACTOR 2
L: NEUTROPHIL CYTOSOL FACTOR 4


Theoretical massNumber of molelcules
Total (without water)22,7892
Polymers22,7892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: NEUTROPHIL CYTOSOL FACTOR 2
M: NEUTROPHIL CYTOSOL FACTOR 4


Theoretical massNumber of molelcules
Total (without water)22,7892
Polymers22,7892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)151.422, 151.422, 68.317
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.5481, 0.8356, -0.0371), (-0.834, -0.5425, 0.1006), (0.064, 0.0861, 0.9942)45.1965, 59.6372, -25.7679
2given(0.98218, -0.11698, -0.14708), (0.10459, 0.9905, -0.089324), (0.15613, 0.07235, 0.98508)-72.088, -17.614, -17.5563
3given(0.656, -0.7527, -0.055), (0.7518, 0.6582, -0.0402), (0.0665, -0.015, 0.9977)23.6739, -66.7072, -24.9095

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Components

#1: Protein
NEUTROPHIL CYTOSOL FACTOR 2 / P67-PHOX


Mass: 9940.824 Da / Num. of mol.: 4 / Fragment: PB1 DOMAIN, RESIDUES 352-429
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPTG / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P19878
#2: Protein
NEUTROPHIL CYTOSOL FACTOR 4 / P40-PHOX


Mass: 12848.079 Da / Num. of mol.: 4 / Fragment: PB1 DOMAIN, RESIDUES 237-339 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPTG / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q15080
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION CYS (242) VAL

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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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growpH: 9
Details: 18% PEG 3350, 17% PEG 400, 4.8% ISOPROPYL ALCOHOL, 0.1 M CAPSO PH 9.0
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.5 mg/mlprotein1drop
220 mMTris1droppH7.4
3100 mM1dropNaCl
45 mMdithiothreitol1drop
518 %PEG33501drop
617 %PEG4001drop
74.8 %isopropanol1drop
80.1 MCAPSO1droppH9.0
918 %PEG33501reservoir
1017 %PEG4001reservoir
110.1 MCAPSO1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97926,0.97912,0.9757959
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2002 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.979121
30.97579591
ReflectionResolution: 2→100 Å / Num. obs: 357868 / % possible obs: 97.7 % / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.6 / % possible all: 94
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 59062 / Num. measured all: 357868 / Rmerge(I) obs: 0.155
Reflection shell
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→100 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.726 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.173
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2957 5 %RANDOM
Rwork0.21 ---
obs0.212 56102 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6032 0 0 343 6375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216114
X-RAY DIFFRACTIONr_bond_other_d0.0070.025556
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9688275
X-RAY DIFFRACTIONr_angle_other_deg0.811312915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026614
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021236
X-RAY DIFFRACTIONr_nbd_refined0.1980.2992
X-RAY DIFFRACTIONr_nbd_other0.2440.26060
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.23456
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8071.53610
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56325864
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.48432504
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0534.52411
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 210
Rwork0.259 3922
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8390.17640.18111.7817-0.48061.3365-0.0211-0.0267-0.07080.00950.02730.0733-0.0486-0.168-0.00630.1359-0.00740.00090.19140.01530.15569.62711.720.409
21.8563-0.6975-0.57625.1568-2.84313.6863-0.1550.0217-0.0433-0.3247-0.1066-0.45910.66440.07610.26160.27070.09840.03840.0458-0.01080.19961.664-1.00522.432
35.2455-0.99091.38232.2916-0.07863.07080.0019-0.3885-0.04050.02880.01130.2908-0.0057-0.2936-0.01310.10650.0019-0.00240.18660.0420.174885.99519.6432.654
41.35951.11760.40412.79911.30373.5972-0.08430.08470.0787-0.1728-0.04950.272-0.5454-0.34280.13370.18930.1434-0.04260.16150.00770.194250.92161.12423.138
51.12750.3134-0.22551.1397-0.7651.09210.01330.025-0.0355-0.0165-0.0248-0.07070.00510.02420.01150.167-0.00870.00290.17450.01570.159733.65511.106-4.098
61.48390.17490.52911.09920.44080.994-0.01430.00320.0103-0.02290.06530.02780.02790.0109-0.05090.16-0.00450.00040.17410.00030.149948.25518.15717.728
71.18890.31560.04161.156-0.65941.33380.0743-0.01480.0344-0.03410.0124-0.02560.0655-0.0401-0.08680.17870.027-0.03780.15890.00980.1516108.87618.04-3.988
81.20040.1957-0.95921.2504-0.2391.4885-0.0246-0.0051-0.033-0.020.0168-0.067-0.0109-0.03530.00790.1496-0.0063-0.01090.16220.00970.169966.0843.35817.143
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A347 - 428
2X-RAY DIFFRACTION2B351 - 427
3X-RAY DIFFRACTION3C352 - 428
4X-RAY DIFFRACTION4D350 - 428
5X-RAY DIFFRACTION5J235 - 339
6X-RAY DIFFRACTION6K236 - 339
7X-RAY DIFFRACTION7L236 - 339
8X-RAY DIFFRACTION8M237 - 339
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 129 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg6.2

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