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- PDB-7szh: Structure of the Rieske Non-heme Iron Oxygenase SxtT with beta-sa... -

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Basic information

Entry
Database: PDB / ID: 7szh
TitleStructure of the Rieske Non-heme Iron Oxygenase SxtT with beta-saxitoxinol Bound
ComponentsSxtT
KeywordsBIOSYNTHETIC PROTEIN / Saxitoxin GxtA Rieske oxygenase metalloprotein iron-sulfur cluster non-heme iron
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding
Similarity search - Function
Vanillate O-demethylase oxygenase-like, C-terminal catalytic domain / Vanillate O-demethylase oxygenase C-terminal domain / : / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
beta-Saxitoxinol / : / FE2/S2 (INORGANIC) CLUSTER / SxtT
Similarity search - Component
Biological speciesMicroseira wollei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsBridwell-Rabb, J. / Liu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM138271 United States
CitationJournal: Nat Commun / Year: 2022
Title: Design principles for site-selective hydroxylation by a Rieske oxygenase.
Authors: Liu, J. / Tian, J. / Perry, C. / Lukowski, A.L. / Doukov, T.I. / Narayan, A.R.H. / Bridwell-Rabb, J.
History
DepositionNov 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SxtT
B: SxtT
C: SxtT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,51642
Polymers115,2983
Non-polymers4,21839
Water14,934829
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13310 Å2
ΔGint-191 kcal/mol
Surface area41280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.282, 158.470, 115.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein SxtT


Mass: 38432.648 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microseira wollei (bacteria) / Gene: sxtT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: C3RVQ0

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Non-polymers , 7 types, 868 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-D82 / beta-Saxitoxinol / [(2Z,3aS,4R,6Z,7S,10S,10aS)-10-hydroxy-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate


Mass: 283.287 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N7O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 829 / 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

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.0 M (NH4)2SO4, 0.1 M Bis-Tris pH 6.5, 10% v/v glycerol, 20 mM beta-saxitoxin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 129304 / % possible obs: 98.5 % / Redundancy: 13.7 % / Biso Wilson estimate: 33.84 Å2 / CC1/2: 1 / Rrim(I) all: 0.068 / Net I/σ(I): 22.05
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.86 / Num. unique obs: 20590 / CC1/2: 0.815 / Rrim(I) all: 1.702 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WN3

6wn3


Resolution: 1.79→48.63 Å / SU ML: 0.2155 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2665
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1985 6489 5.02 %
Rwork0.1706 122814 -
obs0.1721 129303 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.59 Å2
Refinement stepCycle: LAST / Resolution: 1.79→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7826 0 239 829 8894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00728542
X-RAY DIFFRACTIONf_angle_d0.918311673
X-RAY DIFFRACTIONf_chiral_restr0.0611233
X-RAY DIFFRACTIONf_plane_restr0.00611512
X-RAY DIFFRACTIONf_dihedral_angle_d13.75073199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.810.38872000.33353910X-RAY DIFFRACTION94.79
1.81-1.840.33812050.29144092X-RAY DIFFRACTION98.42
1.84-1.860.29232310.27184009X-RAY DIFFRACTION98.67
1.86-1.880.2882340.26394044X-RAY DIFFRACTION98.71
1.88-1.910.28062120.24924074X-RAY DIFFRACTION98.6
1.91-1.930.26011900.24614076X-RAY DIFFRACTION98.36
1.93-1.960.25242130.23483901X-RAY DIFFRACTION94.62
1.96-1.990.27362120.21983879X-RAY DIFFRACTION94.79
1.99-2.020.282070.22354100X-RAY DIFFRACTION99.06
2.02-2.050.24521990.21684085X-RAY DIFFRACTION99.07
2.05-2.090.20892270.18874089X-RAY DIFFRACTION99.01
2.09-2.130.21482000.18924105X-RAY DIFFRACTION99.1
2.13-2.170.24062310.18794079X-RAY DIFFRACTION99.19
2.17-2.210.24692250.1844096X-RAY DIFFRACTION99.24
2.21-2.260.21292190.18674107X-RAY DIFFRACTION99.27
2.26-2.310.24022300.18454086X-RAY DIFFRACTION99.17
2.31-2.370.22762180.18134086X-RAY DIFFRACTION99.33
2.37-2.440.21282000.18214163X-RAY DIFFRACTION99.61
2.44-2.510.23412140.18664147X-RAY DIFFRACTION99.66
2.51-2.590.23032290.18854095X-RAY DIFFRACTION99.36
2.59-2.680.20162120.19614142X-RAY DIFFRACTION99.7
2.68-2.790.20272120.18744023X-RAY DIFFRACTION96.98
2.79-2.910.21472270.17554018X-RAY DIFFRACTION96.65
2.91-3.070.18892130.17644177X-RAY DIFFRACTION99.82
3.07-3.260.20142110.17714155X-RAY DIFFRACTION99.75
3.26-3.510.19922220.15934196X-RAY DIFFRACTION99.91
3.51-3.870.18542210.14534171X-RAY DIFFRACTION99.89
3.87-4.420.15082180.13344238X-RAY DIFFRACTION99.96
4.43-5.570.14442230.13464069X-RAY DIFFRACTION96.19
5.57-48.630.19352340.16464402X-RAY DIFFRACTION99.81

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