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- PDB-7sze: Structure of the Rieske Non-heme Iron Oxygenase GxtA with Saxitox... -

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Basic information

Entry
Database: PDB / ID: 7sze
TitleStructure of the Rieske Non-heme Iron Oxygenase GxtA with Saxitoxin Bound
ComponentsSxtDIOX
KeywordsBIOSYNTHETIC PROTEIN / Saxitoxin GxtA Rieske oxygenase metalloprotein iron-sulfur cluster non-heme iron
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
Chem-9SL / : / FE2/S2 (INORGANIC) CLUSTER / SxtDIOX
Similarity search - Component
Biological speciesMicroseira wollei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)117,71232
Polymers114,7303
Non-polymers2,98229
Water16,916939
1
C: SxtDIOX
hetero molecules

A: SxtDIOX
hetero molecules

B: SxtDIOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,71232
Polymers114,7303
Non-polymers2,98229
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area11380 Å2
ΔGint-204 kcal/mol
Surface area41600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.978, 96.930, 80.672
Angle α, β, γ (deg.)90.000, 106.910, 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 BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: C3RVP5

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Non-polymers , 6 types, 968 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-9SL / [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate / Saxitoxin


Mass: 299.286 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N7O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: toxin*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3 / 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.: 8 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.3 M MgCl2, 0.1 M Bis-Tris pH 5.5, 25% v/v PEG3350, 15% v/v glycerol, 20 mM STX

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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: 1.74→50 Å / Num. obs: 217642 / % possible obs: 96.9 % / Redundancy: 7 % / Biso Wilson estimate: 25.42 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.076 / Net I/σ(I): 16.75
Reflection shellResolution: 1.74→1.84 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.05 / Num. unique obs: 34931 / CC1/2: 0.756 / Rrim(I) all: 1.035 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WNC

6wnc


Resolution: 1.74→46.26 Å / SU ML: 0.1979 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2698
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1965 5546 5.02 %
Rwork0.1605 104917 -
obs0.1623 110463 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.4 Å2
Refinement stepCycle: LAST / Resolution: 1.74→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7826 0 158 939 8923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00778568
X-RAY DIFFRACTIONf_angle_d0.949811743
X-RAY DIFFRACTIONf_chiral_restr0.06631268
X-RAY DIFFRACTIONf_plane_restr0.0081531
X-RAY DIFFRACTIONf_dihedral_angle_d12.83213205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.760.28481810.28143384X-RAY DIFFRACTION94.26
1.76-1.780.29591840.23963491X-RAY DIFFRACTION97.12
1.78-1.80.24451790.22863477X-RAY DIFFRACTION97.26
1.8-1.820.24121890.20683492X-RAY DIFFRACTION97.25
1.82-1.850.2731930.21083415X-RAY DIFFRACTION96.5
1.85-1.870.25591590.20733266X-RAY DIFFRACTION90.3
1.87-1.90.24611820.19083398X-RAY DIFFRACTION94.86
1.9-1.930.24711760.18693551X-RAY DIFFRACTION98.08
1.93-1.960.21251790.18483481X-RAY DIFFRACTION97.97
1.96-1.990.24192110.18773516X-RAY DIFFRACTION97.98
1.99-2.020.20961810.18743502X-RAY DIFFRACTION97.36
2.02-2.060.19691710.17453497X-RAY DIFFRACTION97.27
2.06-2.10.19221900.16643469X-RAY DIFFRACTION97.21
2.1-2.140.211760.16843549X-RAY DIFFRACTION97.92
2.14-2.190.22571970.17333495X-RAY DIFFRACTION97.75
2.19-2.240.22781920.16313495X-RAY DIFFRACTION97.9
2.24-2.290.19561950.17223510X-RAY DIFFRACTION97.63
2.29-2.360.21941770.16833500X-RAY DIFFRACTION96.66
2.36-2.430.19231590.16573283X-RAY DIFFRACTION91.28
2.43-2.50.22131970.16983547X-RAY DIFFRACTION99.18
2.5-2.590.21631850.17073583X-RAY DIFFRACTION99.16
2.59-2.70.21171920.17033546X-RAY DIFFRACTION98.94
2.7-2.820.19341890.16033555X-RAY DIFFRACTION99.05
2.82-2.970.21051830.15853588X-RAY DIFFRACTION98.98
2.97-3.160.19831950.15883557X-RAY DIFFRACTION99.02
3.16-3.40.19241900.15413557X-RAY DIFFRACTION98.19
3.4-3.740.1681900.13743442X-RAY DIFFRACTION95.53
3.74-4.280.15051850.12893597X-RAY DIFFRACTION99.29
4.28-5.390.16091860.12953626X-RAY DIFFRACTION99.01
5.39-46.260.19831830.16923548X-RAY DIFFRACTION96.04

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