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- PDB-3a1f: The crystal structure of NADPH binding domain of gp91(phox) -

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Basic information

Entry
Database: PDB / ID: 3a1f
TitleThe crystal structure of NADPH binding domain of gp91(phox)
ComponentsCytochrome b-245 heavy chain
KeywordsOXIDOREDUCTASE / gp91(phox) / NADPH binding domain
Function / homology
Function and homology information


cellular response to L-glutamine / hypoxia-inducible factor-1alpha signaling pathway / superoxide-generating NAD(P)H oxidase activity / Cross-presentation of particulate exogenous antigens (phagosomes) / perinuclear endoplasmic reticulum / NADPH oxidase complex / respiratory burst / ROS and RNS production in phagocytes / cellular response to ethanol / Oxidoreductases ...cellular response to L-glutamine / hypoxia-inducible factor-1alpha signaling pathway / superoxide-generating NAD(P)H oxidase activity / Cross-presentation of particulate exogenous antigens (phagosomes) / perinuclear endoplasmic reticulum / NADPH oxidase complex / respiratory burst / ROS and RNS production in phagocytes / cellular response to ethanol / Oxidoreductases / superoxide anion generation / response to angiotensin / hydrogen peroxide biosynthetic process / monoatomic ion channel complex / response to aldosterone / superoxide metabolic process / Detoxification of Reactive Oxygen Species / tertiary granule membrane / RHO GTPases Activate NADPH Oxidases / RAC2 GTPase cycle / RAC3 GTPase cycle / specific granule membrane / monoatomic ion transmembrane transport / RAC1 GTPase cycle / cellular response to cadmium ion / response to nutrient / defense response / VEGFA-VEGFR2 Pathway / phagocytic vesicle membrane / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / nuclear envelope / flavin adenine dinucleotide binding / response to xenobiotic stimulus / inflammatory response / protein heterodimerization activity / innate immune response / neuronal cell body / dendrite / heme binding / Neutrophil degranulation / endoplasmic reticulum membrane / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome b245, heavy chain / Ferric reductase, NAD binding domain / Ferric reductase NAD binding domain / FAD-binding 8 / FAD-binding domain / Ferric reductase transmembrane component-like domain / Ferric reductase like transmembrane component / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain ...Cytochrome b245, heavy chain / Ferric reductase, NAD binding domain / Ferric reductase NAD binding domain / FAD-binding 8 / FAD-binding domain / Ferric reductase transmembrane component-like domain / Ferric reductase like transmembrane component / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Cytochrome b-245 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsHonbou, K.
CitationJournal: To be Published
Title: Crystal Structure of NADPH binding domain of gp91(phox)
Authors: Honbou, K. / Noda, N.N. / Sumimoto, H. / Inagaki, F.
History
DepositionApr 1, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome b-245 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5908
Polymers21,1791
Non-polymers4117
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.022, 60.022, 90.398
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-191-

NI

21A-249-

HOH

31A-250-

HOH

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Components

#1: Protein Cytochrome b-245 heavy chain / p22 phagocyte B-cytochrome / Neutrophil cytochrome b 91 kDa NADPH binding domain of human gp91(phox) ...p22 phagocyte B-cytochrome / Neutrophil cytochrome b 91 kDa NADPH binding domain of human gp91(phox) / polypeptide / Heme-binding membrane glycoprotein gp91phox / CGD91-phox / gp91-phox / gp91-1 / Cytochrome b(558) subunit beta / Cytochrome b558 subunit beta / Superoxide-generating NADPH oxidase heavy chain subunit / NADPH oxidase 2


Mass: 21178.758 Da / Num. of mol.: 1 / Fragment: UNP residues 385-570
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P04839
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 12% PEG 3350, 0.1M sodium acetate pH 5.6, 0.4M NiCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 13234 / Num. obs: 13234 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.036
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 9.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→28.48 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 202908.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1331 10.4 %RANDOM
Rwork0.237 ---
obs0.237 12857 97.3 %-
all-12857 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.4501 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.54 Å20 Å20 Å2
2---3.54 Å20 Å2
3---7.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→28.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1277 0 7 72 1356
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 215 10.6 %
Rwork0.276 1808 -
obs--94.6 %
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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