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- PDB-5o0x: Crystal structure of dehydrogenase domain of Cylindrospermum stag... -

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Basic information

Entry
Database: PDB / ID: 5o0x
TitleCrystal structure of dehydrogenase domain of Cylindrospermum stagnale NADPH-Oxidase 5 (NOX5)
ComponentsPutative ferric reductase
KeywordsOXIDOREDUCTASE / Membrane Protein / Reactive Oxygen Species / Oxidative Stress / 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 / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / 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 / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Putative ferric reductase
Similarity search - Component
Biological speciesCylindrospermum stagnale PCC 7417 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMagnani, F. / Nenci, S. / Mattevi, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Science and EducationPRIN2015-20152TE5PK_00 Italy
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Crystal structures and atomic model of NADPH oxidase.
Authors: Magnani, F. / Nenci, S. / Millana Fananas, E. / Ceccon, M. / Romero, E. / Fraaije, M.W. / Mattevi, A.
History
DepositionMay 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative ferric reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,03629
Polymers33,0831
Non-polymers3,95328
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-28 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.279, 128.279, 72.519
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-951-

HOH

21A-959-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative ferric reductase / NOX5


Mass: 33082.906 Da / Num. of mol.: 1 / Fragment: Dehydrogenase domain, UNP residues 413-693
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cylindrospermum stagnale PCC 7417 (bacteria)
Gene: Cylst_1289 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RP+ / References: UniProt: K9WT99

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Non-polymers , 6 types, 127 molecules

#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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 5.24 Å3/Da / Density % sol: 76.54 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 60 mM Ca-acetate, 80 mM NaCacodylate pH 6.5, 12-16% PEG 8000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.2→120 Å / Num. obs: 33160 / % possible obs: 99.3 % / Redundancy: 5.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.237 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3002 / CC1/2: 0.556 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→111.09 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.094 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 1660 4.8 %RANDOM
Rwork0.18427 ---
obs0.18546 33160 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.312 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.3 Å20 Å2
2--0.6 Å2-0 Å2
3----1.96 Å2
Refinement stepCycle: 1 / Resolution: 2.2→111.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 213 99 2378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192321
X-RAY DIFFRACTIONr_bond_other_d0.0030.022183
X-RAY DIFFRACTIONr_angle_refined_deg1.7792.023108
X-RAY DIFFRACTIONr_angle_other_deg0.98735038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1975259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05823.8394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77615331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.471159
X-RAY DIFFRACTIONr_chiral_restr0.0970.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02515
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1374.341042
X-RAY DIFFRACTIONr_mcbond_other3.1394.3381041
X-RAY DIFFRACTIONr_mcangle_it4.7416.491299
X-RAY DIFFRACTIONr_mcangle_other4.746.4931300
X-RAY DIFFRACTIONr_scbond_it3.8734.7511278
X-RAY DIFFRACTIONr_scbond_other3.8734.7511278
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8596.8621810
X-RAY DIFFRACTIONr_long_range_B_refined8.25149.4632537
X-RAY DIFFRACTIONr_long_range_B_other8.2549.4922538
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 140 -
Rwork0.292 2392 -
obs--100 %

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