- PDB-8qq7: Structure of SpNOX: a Bacterial NADPH oxidase -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 8qq7
Title
Structure of SpNOX: a Bacterial NADPH oxidase
Components
FAD-binding FR-type domain-containing protein
Keywords
ELECTRON TRANSPORT / NADPH oxidase / Reactive Oxygen Species production / membrane protein / Streptococcus pneumoniae / F397W mutant / electron transport.
Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest
Y
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 5.11 Å3/Da / Density % sol: 75.95 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Protein: 4.04 mg/ml in 50 mM Tris pH 7, 300 mM NaCl, 0.025 mM MNG3, 0.01 mM FAD. Crystallization condition: 30.5% PEG 300, 0.15 M Li2SO4, 0.15 M NaCl and 0.1 M MES pH6. Drop: 6 uL of protein + 6 uL of well.
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Resolution: 3.62→3.95 Å / Redundancy: 20 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 275 / Rpim(I) all: 0.465 / % possible all: 85.4
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0267
refinement
XDS
datareduction
XSCALE
datascaling
STARANISO
datascaling
PHASER
phasing
Coot
modelbuilding
PDB_EXTRACT
3.27
dataextraction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: model from PROMALS3D and I-TASSER Resolution: 3.62→47.82 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.905 / SU B: 78.364 / SU ML: 1.08 / Cross valid method: THROUGHOUT / ESU R Free: 1.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.32003
245
4.4 %
RANDOM
Rwork
0.26152
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obs
0.2642
5262
47.85 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.6 Å / Solvent model: MASK