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- PDB-5o0t: CRYSTAL STRUCTURE OF TRANS-MEMBRANE DOMAIN OF Cylindrospermum sta... -

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Basic information

Entry
Database: PDB / ID: 5o0t
TitleCRYSTAL STRUCTURE OF TRANS-MEMBRANE DOMAIN OF Cylindrospermum stagnale NADPH-OXIDASE 5 (NOX5)
ComponentsPutative ferric reductase
KeywordsMEMBRANE PROTEIN / Reactive Oxygen Species / Oxidative Stress / 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
DECANE / PROTOPORPHYRIN IX CONTAINING FE / EICOSANE / DI(HYDROXYETHYL)ETHER / Putative ferric reductase
Similarity search - Component
Biological speciesCylindrospermum stagnale PCC 7417 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsMagnani, F. / Nenci, S. / Mattevi, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry for Science and EducationPRIN2015-20152TE5PK_004 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)26,59017
Polymers23,4681
Non-polymers3,12216
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-58 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.371, 74.570, 85.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative ferric reductase


Mass: 23467.914 Da / Num. of mol.: 1 / Mutation: Q207G, K208S, T410A, K411A, E412E
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 , 7 types, 79 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H42
#5: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5
Details: csTM was concentrated to 25 mg-ml and mixed with monoolein (1-oleoyl-rac-glycerol) in a 2:3 protein to lipid ratio using two coupled syringes (Hamilton) at 20 C. The in meso mix was ...Details: csTM was concentrated to 25 mg-ml and mixed with monoolein (1-oleoyl-rac-glycerol) in a 2:3 protein to lipid ratio using two coupled syringes (Hamilton) at 20 C. The in meso mix was dispensed manually using a Hamilton syringe coupled to a repetitive dispenser onto a sandwich plate in 120 nl bolus overlaid by 1 microl of precipitant solution. Crystals grew 30% PEG300, 100 mM Li2SO4, 100 mM MES-KOH pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99997 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.05→44.6 Å / Num. obs: 20900 / % possible obs: 97.6 % / Redundancy: 3.7 % / CC1/2: 0.981 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.3
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1634 / CC1/2: 0.429 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→44.6 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.986 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22094 971 4.7 %RANDOM
Rwork0.18529 ---
obs0.18696 19905 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.363 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--1.29 Å2-0 Å2
3----1.96 Å2
Refinement stepCycle: 1 / Resolution: 2.05→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 205 63 1918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191912
X-RAY DIFFRACTIONr_bond_other_d0.0020.021920
X-RAY DIFFRACTIONr_angle_refined_deg1.662.0412586
X-RAY DIFFRACTIONr_angle_other_deg0.98634376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.845205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70722.42466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0215268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.297155
X-RAY DIFFRACTIONr_chiral_restr0.1160.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022012
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02477
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_it1.4162.475823
X-RAY DIFFRACTIONr_mcbond_other1.4152.481824
X-RAY DIFFRACTIONr_mcangle_it2.1373.7011027
X-RAY DIFFRACTIONr_mcangle_other2.1383.7031028
X-RAY DIFFRACTIONr_scbond_it2.3493.2221089
X-RAY DIFFRACTIONr_scbond_other2.3493.2221089
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6824.5711560
X-RAY DIFFRACTIONr_long_range_B_refined5.37730.3922257
X-RAY DIFFRACTIONr_long_range_B_other5.37630.4252258
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 74 -
Rwork0.241 1461 -
obs--97.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.25980.0819-0.22113.0219-4.80597.67570.02570.0446-0.06990.010.14630.1227-0.023-0.2478-0.1720.0871-0.041-0.01510.06330.03260.0832-6.022-13.7712.123
21.9199-0.5559-1.50950.87370.82973.374-0.0080.1644-0.1369-0.05810.01760.0789-0.0278-0.0703-0.00950.0070.0067-0.00230.1138-0.02210.0756-0.961-3.36-8.929
36.14761.1136-0.95236.0031-2.03294.85290.0269-0.2081-0.13570.2107-0.01410.13270.04150.0839-0.01280.05670.00860.06920.0980.00720.0959-13.6452.60117.394
41.9082-0.1754-1.73090.90560.01793.34140.02370.0234-0.0812-0.00910.0195-0.0614-0.01130.2541-0.04320.00260.0080.00930.1194-0.01010.07387.3181.085-4.577
50.75920.00920.17960.3001-0.31535.0375-0.04970.02970.12350.01830.0176-0.0766-0.2910.25820.03210.0679-0.031-0.02860.04210.01710.06167.31711.1522.329
62.8289-2.9026-3.67343.85324.32796.61920.07420.1598-0.1108-0.0484-0.10.1295-0.2408-0.02140.02580.06570.05440.02420.13440.0380.1051-14.14411.6684.266

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