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- PDB-6wnb: Structure of the Rieske non-heme iron oxygenase SxtT with dideoxy... -

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Basic information

Entry
Database: PDB / ID: 6wnb
TitleStructure of the Rieske non-heme iron oxygenase SxtT with dideoxysaxitoxin bound
ComponentsSxtT
KeywordsBIOSYNTHETIC PROTEIN / saxitoxin / Rieske oxygenase / metalloprotein / natural products
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding / cytoplasm
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] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / Chem-U5A / SxtT
Similarity search - Component
Biological speciesMicroseira wollei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBridwell-Rabb, J. / Liu, J.
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for divergent C-H hydroxylation selectivity in two Rieske oxygenases.
Authors: Lukowski, A.L. / Liu, J. / Bridwell-Rabb, J. / Narayan, A.R.H.
History
DepositionApr 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: 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 / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)118,68832
Polymers115,2983
Non-polymers3,39029
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration shows a trimeric arrangement. Other Rieske oxygenases also adapt trimeric architectures to facilitate electron transfer between the metallocenters.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-261 kcal/mol
Surface area41140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.276, 159.577, 115.979
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
Components on special symmetry positions
IDModelComponents
11C-718-

HOH

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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 (E. coli) / References: UniProt: C3RVQ0

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Non-polymers , 6 types, 471 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.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-U5A / [(2Z,3aS,4R,6Z,10aR)-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate


Mass: 267.288 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N7O2 / 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.: 13 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 3.06 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.0 M (NH4)2SO4, 0.1 M Bis-Tris pH 6.5, 10% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30.16 Å / Num. obs: 81796 / % possible obs: 98.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 36.45 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.8
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 8066 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WN3

6wn3


Resolution: 2.1→30.16 Å / SU ML: 0.2202 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.6312
RfactorNum. reflection% reflection
Rfree0.2075 4111 5.03 %
Rwork0.1684 --
obs0.1704 81772 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7792 0 179 442 8413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00798480
X-RAY DIFFRACTIONf_angle_d0.970911628
X-RAY DIFFRACTIONf_chiral_restr0.05761230
X-RAY DIFFRACTIONf_plane_restr0.00621516
X-RAY DIFFRACTIONf_dihedral_angle_d18.87913153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.31561190.24112621X-RAY DIFFRACTION97.4
2.12-2.150.26341540.2192645X-RAY DIFFRACTION99.43
2.15-2.180.29351500.21592661X-RAY DIFFRACTION99.89
2.18-2.210.25131440.22656X-RAY DIFFRACTION99.82
2.21-2.240.26991410.19892667X-RAY DIFFRACTION99.93
2.24-2.270.24881410.19352664X-RAY DIFFRACTION99.86
2.27-2.30.25191480.19092649X-RAY DIFFRACTION99.86
2.3-2.340.24671460.18662664X-RAY DIFFRACTION99.68
2.34-2.380.25831400.18682680X-RAY DIFFRACTION99.79
2.38-2.420.24211360.19452692X-RAY DIFFRACTION99.61
2.42-2.460.27651350.19442671X-RAY DIFFRACTION99.64
2.46-2.510.26441320.19532657X-RAY DIFFRACTION99.43
2.51-2.560.23861400.19132659X-RAY DIFFRACTION99.01
2.56-2.620.22961390.18732653X-RAY DIFFRACTION99.32
2.62-2.680.21941470.18182659X-RAY DIFFRACTION99.12
2.68-2.740.23391420.182656X-RAY DIFFRACTION99.11
2.74-2.820.20191330.1892689X-RAY DIFFRACTION98.95
2.82-2.90.26591560.19672665X-RAY DIFFRACTION99.26
2.9-2.990.24921200.18862644X-RAY DIFFRACTION98.5
2.99-3.10.22841540.1882664X-RAY DIFFRACTION99.82
3.1-3.220.20851360.18522713X-RAY DIFFRACTION99.75
3.23-3.370.22311450.18292689X-RAY DIFFRACTION99.86
3.37-3.550.19611440.16582712X-RAY DIFFRACTION99.79
3.55-3.770.21351420.16122697X-RAY DIFFRACTION99.86
3.77-4.060.17621400.14082710X-RAY DIFFRACTION99.79
4.06-4.470.1491430.13142742X-RAY DIFFRACTION99.72
4.47-5.110.14381450.12662678X-RAY DIFFRACTION98.47
5.11-6.430.19721540.15652709X-RAY DIFFRACTION97.71
6.43-30.160.19211450.1622795X-RAY DIFFRACTION97.19

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