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- PDB-8cap: Crystal structure of dehydrogenase domain of Cylindrospermum stag... -

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Basic information

Entry
Database: PDB / ID: 8cap
TitleCrystal structure of dehydrogenase domain of Cylindrospermum stagnale NADPH-Oxidase 5 (NOX5) in complex with CB28
ComponentsPutative ferric reductase
KeywordsOXIDOREDUCTASE / ROS / inhibitor / redox biology
Function / homology
Function and homology information


oxidoreductase activity / calcium ion binding / membrane
Similarity search - Function
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 / EF-hand domain pair / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. ...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 / EF-hand domain pair / 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 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-U4O / Putative ferric reductase
Similarity search - Component
Biological speciesCylindrospermum stagnale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsReis, J. / Mattevi, A.
Funding support Italy, 2items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG19808 Italy
Italian Association for Cancer Research800924 Italy
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: Targeting ROS production through inhibition of NADPH oxidases.
Authors: Reis, J. / Gorgulla, C. / Massari, M. / Marchese, S. / Valente, S. / Noce, B. / Basile, L. / Torner, R. / Cox 3rd, H. / Viennet, T. / Yang, M.H. / Ronan, M.M. / Rees, M.G. / Roth, J.A. / ...Authors: Reis, J. / Gorgulla, C. / Massari, M. / Marchese, S. / Valente, S. / Noce, B. / Basile, L. / Torner, R. / Cox 3rd, H. / Viennet, T. / Yang, M.H. / Ronan, M.M. / Rees, M.G. / Roth, J.A. / Capasso, L. / Nebbioso, A. / Altucci, L. / Mai, A. / Arthanari, H. / Mattevi, A.
History
DepositionJan 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ferric reductase
B: Putative ferric reductase
C: Putative ferric reductase
E: Putative ferric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,98012
Polymers128,9244
Non-polymers5,0568
Water0
1
A: Putative ferric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4953
Polymers32,2311
Non-polymers1,2642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative ferric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4953
Polymers32,2311
Non-polymers1,2642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative ferric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4953
Polymers32,2311
Non-polymers1,2642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Putative ferric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4953
Polymers32,2311
Non-polymers1,2642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.835, 88.222, 98.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain E

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA413 - 801
211chain BB413 - 901
311chain CC413 - 901
411chain EE413 - 901

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Components

#1: Protein
Putative ferric reductase


Mass: 32230.916 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cylindrospermum stagnale (bacteria) / Gene: Cylst_1289 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: K9WT99
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-U4O / [4-[[(4~{E})-4-(furan-2-ylmethylidene)-2,3-dihydro-1~{H}-acridin-9-yl]carbonyl]piperazin-1-yl]-pyridin-2-yl-methanone


Mass: 478.542 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H26N4O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: Hepes 0.1 mM pH 7.5, 0.3 M sodium nitrate, 0.3 M disodium hydrogen phosphate, 0.3 M ammonium sulfate, 20% (v/v) glycerol, 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 3→49.024 Å / Num. obs: 24161 / % possible obs: 96.4 % / Redundancy: 4.6 % / CC1/2: 0.986 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.124 / Rrim(I) all: 0.284 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.182.71.631915134220.251.1582.0110.685.4
9-49.0250.0647579590.9970.0290.06717.398.3

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.024 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2955 1169 4.86 %
Rwork0.2389 22897 -
obs0.2416 24066 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.82 Å2 / Biso mean: 72.1108 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3→49.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7818 0 356 0 8174
Biso mean--72.84 --
Num. residues----976
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2352X-RAY DIFFRACTION5.249TORSIONAL
12B2352X-RAY DIFFRACTION5.249TORSIONAL
13C2352X-RAY DIFFRACTION5.249TORSIONAL
14E2352X-RAY DIFFRACTION5.249TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.13660.4671260.389250184
3.1366-3.30190.34811150.3181259687
3.3019-3.50870.32841770.27082929100
3.5087-3.77950.3231540.25042945100
3.7795-4.15970.31031620.23982944100
4.1597-4.76120.25111440.2092297199
4.7612-5.99690.28541350.2213012100
5.9969-49.0240.25951560.213299998

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