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

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Basic information

Entry
Database: PDB / ID: 8cao
TitleCrystal structure of dehydrogenase domain of Cylindrospermum stagnale NADPH-Oxidase 5 (NOX5) in complex with CA24
ComponentsPutative ferric reductase
KeywordsOXIDOREDUCTASE / ROS / inhibitor / redox biology
Function / homology
Function and homology information


superoxide-generating NAD(P)H oxidase activity / NADPH oxidase complex / superoxide anion generation / defense response / nucleotide binding / calcium ion binding
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 ...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 / DI(HYDROXYETHYL)ETHER / Chem-U40 / Putative ferric reductase
Similarity search - Component
Biological speciesCylindrospermum stagnale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7679
Polymers33,0831
Non-polymers1,6858
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint9 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.428, 127.428, 71.992
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-906-

HOH

21A-914-

HOH

31A-928-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative ferric reductase


Mass: 33082.906 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

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Non-polymers , 5 types, 36 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-U40 / 8-[2-(4-cyclohexylphenyl)quinolin-4-yl]carbonyl-1,3,8-triazaspiro[4.5]decane-2,4-dione


Mass: 482.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H30N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 6.5
Details: MES 0.1 mM pH 6.5, 0.1 M carboxylic acids, 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: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2.3→47.76 Å / Num. obs: 30148 / % possible obs: 99.7 % / Redundancy: 4.2 % / CC1/2: 0.964 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.106 / Rrim(I) all: 0.231 / Net I/σ(I): 4.2
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
2.3-2.384.21.1761238129150.4480.6271.3421.299.7
8.91-47.714.10.14123245640.9510.0820.1658.897.3

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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: 2.3→47.76 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.14 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 1530 5.1 %RANDOM
Rwork0.2164 ---
obs0.217 28597 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 164.96 Å2 / Biso mean: 56.8627 Å2 / Biso min: 27.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.59 Å20 Å2
2--1.18 Å2-0 Å2
3----3.84 Å2
Refinement stepCycle: final / Resolution: 2.3→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 116 28 2156
Biso mean--60.3 46.74 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132192
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172004
X-RAY DIFFRACTIONr_angle_refined_deg2.0741.6772985
X-RAY DIFFRACTIONr_angle_other_deg1.3981.5984618
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 1 (DEGREES)8.0465253
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 2 (DEGREES)34.5922.6100
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 3 (DEGREES)16.7315325
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 4 (DEGREES)19.443159
X-RAY DIFFRACTIONr_chiral_restr0.2070.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022420
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02503
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 99 -
Rwork0.339 2137 -
all-2236 -
obs--99.64 %

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