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- PDB-7szg: Structure of the Rieske Non-heme Iron Oxygenase GxtA Pressurized ... -

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Basic information

Entry
Database: PDB / ID: 7szg
TitleStructure of the Rieske Non-heme Iron Oxygenase GxtA Pressurized with Xenon
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / FE2/S2 (INORGANIC) CLUSTER / XENON / SxtDIOX
Similarity search - Component
Biological speciesMicroseira wollei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,94124
Polymers114,7303
Non-polymers2,21121
Water4,594255
1
A: SxtDIOX
hetero molecules

B: SxtDIOX
hetero molecules

C: SxtDIOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,94124
Polymers114,7303
Non-polymers2,21121
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area11340 Å2
ΔGint-174 kcal/mol
Surface area40270 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

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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 , 7 types, 276 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.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Xe / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 49.59 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 2.06633 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.06633 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 59952 / % possible obs: 99.7 % / Redundancy: 18.5 % / Biso Wilson estimate: 55.26 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.141 / Net I/σ(I): 19.63
Reflection shellResolution: 2.69→2.76 Å / Redundancy: 17.45 % / Mean I/σ(I) obs: 2.42 / Num. unique obs: 4447 / CC1/2: 0.793 / Rrim(I) all: 1.393 / % possible all: 100

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Processing

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

6wnc


Resolution: 2.69→48.47 Å / SU ML: 0.4168 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0309
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2436 2995 5.01 %
Rwork0.2049 56821 -
obs0.2067 59816 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.65 Å2
Refinement stepCycle: LAST / Resolution: 2.69→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7705 0 81 255 8041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01128000
X-RAY DIFFRACTIONf_angle_d1.57910902
X-RAY DIFFRACTIONf_chiral_restr0.09891196
X-RAY DIFFRACTIONf_plane_restr0.00791394
X-RAY DIFFRACTIONf_dihedral_angle_d16.67222935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.730.46121290.42522449X-RAY DIFFRACTION89.95
2.73-2.780.40261600.38962691X-RAY DIFFRACTION100
2.78-2.830.43391280.33392734X-RAY DIFFRACTION100
2.83-2.890.3571470.2892730X-RAY DIFFRACTION99.86
2.89-2.950.38681230.26272707X-RAY DIFFRACTION99.4
2.95-3.010.29511660.24292710X-RAY DIFFRACTION99.86
3.01-3.080.29411420.23232735X-RAY DIFFRACTION99.9
3.08-3.160.2731460.23222678X-RAY DIFFRACTION100
3.16-3.240.31511460.2472759X-RAY DIFFRACTION100
3.24-3.340.30611420.25432717X-RAY DIFFRACTION99.48
3.34-3.440.32891380.26992709X-RAY DIFFRACTION99.82
3.44-3.570.22061410.21452756X-RAY DIFFRACTION99.97
3.57-3.710.1961710.1922712X-RAY DIFFRACTION100
3.71-3.880.19621300.1732683X-RAY DIFFRACTION99.58
3.88-4.080.20941380.16412758X-RAY DIFFRACTION99.86
4.08-4.340.18961500.15882695X-RAY DIFFRACTION100
4.34-4.670.20681410.15572730X-RAY DIFFRACTION99.72
4.68-5.140.20421440.15442696X-RAY DIFFRACTION99.86
5.14-5.890.21111380.19012726X-RAY DIFFRACTION99.9
5.89-7.410.24031460.21082745X-RAY DIFFRACTION99.76
7.41-48.470.21371290.17712701X-RAY DIFFRACTION99.26

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