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- PDB-8pz5: Structure of ThcOx, solved at wavelength 3.099 A -

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Basic information

Entry
Database: PDB / ID: 8pz5
TitleStructure of ThcOx, solved at wavelength 3.099 A
ComponentsSagB-type dehydrogenase domain protein
KeywordsOXIDOREDUCTASE / oxidase
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
ThcOx helix turn helix domain / : / ThcOx helix turn helix domain / Cyanobactin oxidase ThcOx, / SagB-type dehydrogenase domain / : / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / SagB-type dehydrogenase domain protein
Similarity search - Component
Biological speciesCyanothece sp. PCC 7425 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsDuman, R. / El Omari, K. / Mykhaylyk, V. / Orr, C. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SagB-type dehydrogenase domain protein
B: SagB-type dehydrogenase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6774
Polymers105,7642
Non-polymers9132
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-43 kcal/mol
Surface area38250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.390, 111.390, 217.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein SagB-type dehydrogenase domain protein


Mass: 52882.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. PCC 7425 (bacteria) / Gene: Cyan7425_0520 / Production host: Escherichia coli (E. coli) / References: UniProt: B8HTZ1
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / 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: 3.19 Å3/Da / Density % sol: 61.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.75 / Details: 1.0 M sodium citrate, 0.1 M CHES pH 7.75

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.099 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Feb 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 3.099 Å / Relative weight: 1
ReflectionResolution: 3.2→77.82 Å / Num. obs: 39731 / % possible obs: 91.63 % / Redundancy: 25.8 % / Biso Wilson estimate: 134.59 Å2 / CC1/2: 0.999 / Net I/σ(I): 29.98
Reflection shellResolution: 3.2→3.315 Å / Num. unique obs: 1817 / CC1/2: 0.722

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→77.82 Å / SU ML: 0.5076 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5201
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2355 3728 9.38 %
Rwork0.2068 36003 -
obs0.2096 39731 92.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 140.18 Å2
Refinement stepCycle: LAST / Resolution: 3.2→77.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7224 0 62 0 7286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00197460
X-RAY DIFFRACTIONf_angle_d0.501610187
X-RAY DIFFRACTIONf_chiral_restr0.0391184
X-RAY DIFFRACTIONf_plane_restr0.00411285
X-RAY DIFFRACTIONf_dihedral_angle_d17.08612703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.240.52761170.45161153X-RAY DIFFRACTION79.28
3.24-3.280.43951240.41851182X-RAY DIFFRACTION80.87
3.28-3.330.34721210.36331138X-RAY DIFFRACTION81.07
3.33-3.380.33981270.32561225X-RAY DIFFRACTION82.69
3.38-3.430.38651210.30171169X-RAY DIFFRACTION82.85
3.43-3.480.33311280.28681268X-RAY DIFFRACTION84.71
3.48-3.540.2831290.26151212X-RAY DIFFRACTION85.58
3.54-3.60.33741320.24211274X-RAY DIFFRACTION87.22
3.6-3.660.29851310.24891262X-RAY DIFFRACTION87.45
3.66-3.730.25021300.24721269X-RAY DIFFRACTION88.66
3.73-3.810.30531360.25881291X-RAY DIFFRACTION90.32
3.81-3.890.29291390.26681344X-RAY DIFFRACTION91.6
3.89-3.980.34991390.25511356X-RAY DIFFRACTION93.15
3.98-4.080.25861410.23011373X-RAY DIFFRACTION94.86
4.08-4.190.24851390.20331378X-RAY DIFFRACTION95.95
4.19-4.320.23731400.18861407X-RAY DIFFRACTION96.99
4.32-4.460.22891480.16761424X-RAY DIFFRACTION97.1
4.46-4.620.25251440.17841406X-RAY DIFFRACTION97.12
4.62-4.80.20261450.18441420X-RAY DIFFRACTION97.81
4.8-5.020.21761450.17071410X-RAY DIFFRACTION98.05
5.02-5.280.19811510.17831434X-RAY DIFFRACTION98.39
5.28-5.610.26161500.19481414X-RAY DIFFRACTION98.68
5.62-6.050.22751480.21441425X-RAY DIFFRACTION98.87
6.05-6.650.2481470.22781442X-RAY DIFFRACTION99.5
6.66-7.620.23441500.20951442X-RAY DIFFRACTION99.5
7.62-9.590.16961520.17571442X-RAY DIFFRACTION100
9.6-77.820.20341540.18831443X-RAY DIFFRACTION99.38

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