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- PDB-6wnd: Structure of the Rieske non-heme iron oxygenase GxtA with dideoxy... -

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Basic information

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


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / 2 iron, 2 sulfur cluster binding / 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. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich ...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. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / Chem-U5A / SxtDIOX
Similarity search - Component
Biological speciesMicroseira wollei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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.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)117,65830
Polymers114,7303
Non-polymers2,92827
Water5,368298
1
A: SxtDIOX
hetero molecules

B: SxtDIOX
hetero molecules

C: SxtDIOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,65830
Polymers114,7303
Non-polymers2,92827
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 area11360 Å2
ΔGint-164 kcal/mol
Surface area40510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.578, 96.976, 80.409
Angle α, β, γ (deg.)90.000, 107.241, 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

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Protein , 1 types, 3 molecules ABC

#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

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Non-polymers , 6 types, 325 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.: 14 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
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-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.18→41.47 Å / Num. obs: 56610 / % possible obs: 99.43 % / Redundancy: 3.8 % / Biso Wilson estimate: 33.96 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.3
Reflection shellResolution: 2.182→2.26 Å / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 5402 / CC1/2: 0.607 / % possible all: 94.59

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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: 6WNC

6wnc


Resolution: 2.18→41.47 Å / SU ML: 0.2778 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2069
RfactorNum. reflection% reflection
Rfree0.208 2835 5.01 %
Rwork0.1684 --
obs0.1737 56608 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.16 Å2
Refinement stepCycle: LAST / Resolution: 2.18→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7690 0 160 298 8148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00798085
X-RAY DIFFRACTIONf_angle_d0.969811021
X-RAY DIFFRACTIONf_chiral_restr0.05571198
X-RAY DIFFRACTIONf_plane_restr0.0061414
X-RAY DIFFRACTIONf_dihedral_angle_d19.08152997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.220.3261390.23152365X-RAY DIFFRACTION89.02
2.22-2.260.29851390.22372759X-RAY DIFFRACTION100
2.26-2.30.27191510.22782649X-RAY DIFFRACTION100
2.3-2.350.29651290.21812688X-RAY DIFFRACTION100
2.35-2.40.29791350.20772691X-RAY DIFFRACTION99.96
2.4-2.460.27131490.2012658X-RAY DIFFRACTION100
2.46-2.520.26641390.20292725X-RAY DIFFRACTION100
2.52-2.590.27331450.19542705X-RAY DIFFRACTION100
2.59-2.660.2621340.18882701X-RAY DIFFRACTION100
2.66-2.750.23191450.17672653X-RAY DIFFRACTION100
2.75-2.850.2531490.17172736X-RAY DIFFRACTION100
2.85-2.960.261300.18232696X-RAY DIFFRACTION100
2.96-3.10.26991520.17392678X-RAY DIFFRACTION100
3.1-3.260.25171440.17312700X-RAY DIFFRACTION100
3.26-3.460.22391410.16362712X-RAY DIFFRACTION100
3.46-3.730.2171490.15482709X-RAY DIFFRACTION100
3.73-4.110.21741360.1482706X-RAY DIFFRACTION100
4.11-4.70.15671460.13222730X-RAY DIFFRACTION100
4.7-5.920.18981390.15632728X-RAY DIFFRACTION100
5.92-41.470.22561440.17882784X-RAY DIFFRACTION99.93

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