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

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Basic information

Entry
Database: PDB / ID: 8cal
TitleCrystal structure of dehydrogenase domain of Cylindrospermum stagnale NADPH-Oxidase 5 (NOX5) in complex with M34
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-U45 / Putative ferric reductase
Similarity search - Component
Biological speciesCylindrospermum stagnale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5074
Polymers32,2311
Non-polymers1,2763
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-5 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.241, 127.241, 71.888
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Putative ferric reductase


Mass: 32230.916 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-U45 / 3-[(2~{R})-3-carbazol-9-yl-2-oxidanyl-propyl]-4-oxidanylidene-phthalazine-1-carboxamide


Mass: 412.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20N4O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 293 K / Method: evaporation / pH: 8
Details: 0.3 M diethylene glycol; 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol, Tris-HCl 0.1 M pH 8.0, 20% (v/v) ethylene glycol, 10% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 2.41→47.69 Å / Num. obs: 26237 / % possible obs: 99.9 % / Redundancy: 20.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.031 / Rrim(I) all: 0.141 / Net I/σ(I): 17
Reflection shell

Diffraction-ID: 1 / Redundancy: 19.5 % / % possible all: 99.4

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.41-2.52.6815263426950.7070.6152.7521.4
9.01-47.640.0311077055310.0070.03274

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→47.69 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.863 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1235 4.7 %RANDOM
Rwork0.2079 ---
obs0.2095 25000 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 209.34 Å2 / Biso mean: 67.6855 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20.68 Å20 Å2
2--1.36 Å2-0 Å2
3----4.41 Å2
Refinement stepCycle: final / Resolution: 2.41→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 88 10 2119
Biso mean--66.44 57.47 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132181
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171974
X-RAY DIFFRACTIONr_angle_refined_deg1.991.6722982
X-RAY DIFFRACTIONr_angle_other_deg1.3221.5884544
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 1 (DEGREES)8.115254
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 2 (DEGREES)35.63122.574101
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 3 (DEGREES)17.82515326
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 4 (DEGREES)20.599159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022440
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02512
LS refinement shellResolution: 2.41→2.471 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.416 81 -
Rwork0.336 1824 -
obs--99.22 %

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