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- PDB-7cfz: SH3 domain of NADPH oxidase activator 1 -

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Basic information

Entry
Database: PDB / ID: 7cfz
TitleSH3 domain of NADPH oxidase activator 1
ComponentsNADPH oxidase activator 1
KeywordsCYTOSOLIC PROTEIN / SH3 / NOXA1 / NADPH oxidase activator 1
Function / homology
Function and homology information


superoxide-generating NADPH oxidase activator activity / regulation of respiratory burst / NADPH oxidase complex / regulation of hydrogen peroxide metabolic process / WNT5:FZD7-mediated leishmania damping / superoxide anion generation / superoxide metabolic process / CDC42 GTPase cycle / RHO GTPases Activate NADPH Oxidases / RAC3 GTPase cycle ...superoxide-generating NADPH oxidase activator activity / regulation of respiratory burst / NADPH oxidase complex / regulation of hydrogen peroxide metabolic process / WNT5:FZD7-mediated leishmania damping / superoxide anion generation / superoxide metabolic process / CDC42 GTPase cycle / RHO GTPases Activate NADPH Oxidases / RAC3 GTPase cycle / RAC1 GTPase cycle / small GTPase binding / SH3 domain binding / enzyme binding / identical protein binding / cytosol
Similarity search - Function
NADPH oxidase activator 1 / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / SH3 domain / Src homology 3 domains ...NADPH oxidase activator 1 / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
NADPH oxidase activator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsKim, M. / Park, J.H. / Attri, P. / Lee, W.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural modification of NADPH oxidase activator (Noxa 1) by oxidative stress: An experimental and computational study.
Authors: Attri, P. / Park, J.H. / De Backer, J. / Kim, M. / Yun, J.H. / Heo, Y. / Dewilde, S. / Shiratani, M. / Choi, E.H. / Lee, W. / Bogaerts, A.
History
DepositionJun 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH oxidase activator 1
B: NADPH oxidase activator 1


Theoretical massNumber of molelcules
Total (without water)14,2222
Polymers14,2222
Non-polymers00
Water86548
1
A: NADPH oxidase activator 1


Theoretical massNumber of molelcules
Total (without water)7,1111
Polymers7,1111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH oxidase activator 1


Theoretical massNumber of molelcules
Total (without water)7,1111
Polymers7,1111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.596, 49.014, 72.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-121-

HOH

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Components

#1: Protein NADPH oxidase activator 1 / NOX activator 1 / Antigen NY-CO-31 / NCF2-like protein / P67phox-like factor / p51-nox


Mass: 7111.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOXA1, P51NOX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86UR1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.92 Å3/Da / Density % sol: 35.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.2M Magnesium chloride hexahydrate, 25% PEG 3,350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.885→50 Å / Num. obs: 9201 / % possible obs: 98.57 % / Redundancy: 5 % / Biso Wilson estimate: 33.09 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 27.2
Reflection shellResolution: 1.885→1.96 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 225 / % possible all: 98.22

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Processing

Software
NameVersionClassification
HKL-20001.13_2998data scaling
PHASER1.13_2998phasing
Cootmodel building
PHENIX1.13-2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k28

5k28


Resolution: 1.89→40.68 Å / SU ML: 0.2188 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.303 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2555 920 10 %
Rwork0.227 8276 -
obs0.2298 9196 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.39 Å2
Refinement stepCycle: LAST / Resolution: 1.89→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 0 48 957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034933
X-RAY DIFFRACTIONf_angle_d0.69541270
X-RAY DIFFRACTIONf_chiral_restr0.0508135
X-RAY DIFFRACTIONf_plane_restr0.0042170
X-RAY DIFFRACTIONf_dihedral_angle_d3.0669539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.980.27981270.27141150X-RAY DIFFRACTION98.69
1.98-2.110.25251300.25341160X-RAY DIFFRACTION99.61
2.11-2.270.27981300.24331173X-RAY DIFFRACTION99.16
2.27-2.50.29931300.22951171X-RAY DIFFRACTION98.94
2.5-2.860.27581300.24681171X-RAY DIFFRACTION98.41
2.86-3.610.25781340.22281198X-RAY DIFFRACTION98.38
3.61-40.680.23331390.21221253X-RAY DIFFRACTION97

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