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- PDB-6wnc: Structure of the Rieske non-heme iron oxygenase GxtA -

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Basic information

Entry
Database: PDB / ID: 6wnc
TitleStructure of the Rieske non-heme iron oxygenase GxtA
ComponentsSxtDIOX
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 / SxtDIOX
Similarity search - Component
Biological speciesMicroseira wollei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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: SxtDIOX
B: SxtDIOX
C: SxtDIOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,60911
Polymers114,7303
Non-polymers8798
Water6,431357
1
A: SxtDIOX
hetero molecules

B: SxtDIOX
hetero molecules

C: SxtDIOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,60911
Polymers114,7303
Non-polymers8798
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area8460 Å2
ΔGint-128 kcal/mol
Surface area41790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.730, 96.932, 80.809
Angle α, β, γ (deg.)90.000, 106.967, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein SxtDIOX


Mass: 38243.387 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microseira wollei (bacteria) / Gene: sxtDIOX / Production host: Escherichia coli (E. coli) / References: UniProt: C3RVP5
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.3 M MgCl2, 0.1 M Bis-Tris pH 5.5, 25% v/v PEG3350, 15% 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: 0.9787 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 54048 / % possible obs: 96.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 36.91 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.186 / Net I/σ(I): 10.56
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 5122 / CC1/2: 0.73 / % possible all: 90.9

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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: 2.2→38.65 Å / SU ML: 0.228 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.6905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2188 2701 5 %
Rwork0.1942 51327 -
obs0.1954 54028 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.74 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7691 0 27 357 8075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01128011
X-RAY DIFFRACTIONf_angle_d1.535210942
X-RAY DIFFRACTIONf_chiral_restr0.08341201
X-RAY DIFFRACTIONf_plane_restr0.01261409
X-RAY DIFFRACTIONf_dihedral_angle_d18.3452941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.26461370.24072518X-RAY DIFFRACTION91.08
2.24-2.280.241440.23782595X-RAY DIFFRACTION94.06
2.28-2.330.25731430.2282654X-RAY DIFFRACTION94.85
2.33-2.380.2641340.23132680X-RAY DIFFRACTION95.75
2.38-2.440.26691360.23292657X-RAY DIFFRACTION95.95
2.44-2.50.28691450.23172696X-RAY DIFFRACTION95.79
2.5-2.560.27721290.22742549X-RAY DIFFRACTION91.96
2.56-2.640.23961380.21982657X-RAY DIFFRACTION95.62
2.64-2.720.24141480.20982781X-RAY DIFFRACTION99.12
2.72-2.820.25961470.20512762X-RAY DIFFRACTION99.32
2.82-2.930.24291400.20772784X-RAY DIFFRACTION99.35
2.94-3.070.23541560.1962757X-RAY DIFFRACTION99.12
3.07-3.230.23571470.19292794X-RAY DIFFRACTION99.02
3.23-3.430.23381450.18452763X-RAY DIFFRACTION98.78
3.43-3.70.20161510.17182732X-RAY DIFFRACTION97.83
3.7-4.070.17531370.16482739X-RAY DIFFRACTION97.16
4.07-4.660.16721400.15882642X-RAY DIFFRACTION94.24
4.66-5.860.1791400.1812706X-RAY DIFFRACTION95.86
5.87-38.650.24051440.21642861X-RAY DIFFRACTION99.17

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