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- PDB-8evo: Sulfatase from Mycobacterium tuberculosis (Rv3406) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8evo
TitleSulfatase from Mycobacterium tuberculosis (Rv3406) in complex with inhibitor FG2216
ComponentsAlpha-ketoglutarate-dependent sulfate ester dioxygenase
KeywordsOXIDOREDUCTASE/INHIBITOR / oxidoreductase-inhibitor complex / sulfatase / 2-oxoglutarate dependent dioxygenase
Function / homology
Function and homology information


alkyl sulfatase / 2-oxoglutarate-dependent dioxygenase activity / response to antibiotic / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Chem-UN9 / Alpha-ketoglutarate-dependent sulfate ester dioxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJuan, T.-J. / Leung, I. / Squire, C.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Not funded New Zealand
CitationJournal: To Be Published
Title: Sulfatase from Mycobacterium tuberculosis (Rv3406) in complex with inhibitors NOG and FG2216
Authors: Juan, T.-J. / Leung, I. / Squire, C.J.
History
DepositionOct 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent sulfate ester dioxygenase
B: Alpha-ketoglutarate-dependent sulfate ester dioxygenase
C: Alpha-ketoglutarate-dependent sulfate ester dioxygenase
D: Alpha-ketoglutarate-dependent sulfate ester dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,1209
Polymers131,6054
Non-polymers5155
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.040, 129.006, 138.355
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Alpha-ketoglutarate-dependent sulfate ester dioxygenase / Type II alkyl sulfatase


Mass: 32901.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv3406, MTCY78.22c / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli)
References: UniProt: P9WKZ1, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-UN9 / N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE


Mass: 280.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9ClN2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 16% PEG2000, 100 mM Tris, pH 8.5, 2% MPD, 300 mM magnesium nitrate

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.4→47.43 Å / Num. obs: 46395 / % possible obs: 100 % / Redundancy: 52.6 % / CC1/2: 0.998 / Rpim(I) all: 0.07 / Net I/σ(I): 9.5
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 52.4 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4474 / CC1/2: 0.652 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4FFA

4ffa


Resolution: 2.4→47.43 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / SU B: 17.48 / SU ML: 0.35 / Cross valid method: FREE R-VALUE / ESU R: 0.438 / ESU R Free: 0.291
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2889 2281 4.924 %taken from previous in-house structure
Rwork0.2465 44046 --
all0.249 ---
obs-46327 99.937 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 65.466 Å2
Baniso -1Baniso -2Baniso -3
1-9.709 Å20 Å20 Å2
2---4.639 Å20 Å2
3----5.069 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7440 0 23 19 7482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0127653
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166856
X-RAY DIFFRACTIONr_angle_refined_deg0.7341.63510412
X-RAY DIFFRACTIONr_angle_other_deg0.2661.55215872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.7371076
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.963101157
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.82310368
X-RAY DIFFRACTIONr_chiral_restr0.0330.21165
X-RAY DIFFRACTIONr_chiral_restr_other0.0240.23
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028899
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021592
X-RAY DIFFRACTIONr_nbd_refined0.1930.21384
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.26565
X-RAY DIFFRACTIONr_nbtor_refined0.1670.23607
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24039
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2188
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0750.23
X-RAY DIFFRACTIONr_nbd_other0.10.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0560.21
X-RAY DIFFRACTIONr_mcbond_it2.2266.753800
X-RAY DIFFRACTIONr_mcbond_other2.2246.7493799
X-RAY DIFFRACTIONr_mcangle_it3.83310.1044729
X-RAY DIFFRACTIONr_mcangle_other3.83210.1054730
X-RAY DIFFRACTIONr_scbond_it2.1186.9143853
X-RAY DIFFRACTIONr_scbond_other2.1186.9153853
X-RAY DIFFRACTIONr_scangle_it3.48110.2845683
X-RAY DIFFRACTIONr_scangle_other3.4810.2855684
X-RAY DIFFRACTIONr_lrange_it5.92278.1338144
X-RAY DIFFRACTIONr_lrange_other5.92278.1418145
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.4761620.41932010.42133720.6820.72499.73310.384
2.462-2.5290.4431750.39631210.39932960.7340.7741000.356
2.529-2.6020.3671580.38830340.38731920.8090.8011000.353
2.602-2.6820.3731570.36729400.36730970.6980.7261000.333
2.682-2.770.3711360.35128760.35230120.8550.8361000.317
2.77-2.8670.3371330.31427870.31529200.8940.891000.283
2.867-2.9750.311570.27826710.2828290.9380.93199.96470.258
2.975-3.0960.31220.26926100.2727320.9350.9481000.253
3.096-3.2330.2951280.24924780.25126060.9360.9551000.238
3.233-3.390.2811260.22923910.23225170.9520.9641000.222
3.39-3.5720.2721190.2122640.21323830.9550.9691000.207
3.572-3.7870.271060.20721510.2122570.9520.9711000.207
3.787-4.0470.2871120.20620320.2121440.9530.971000.213
4.047-4.3690.213910.18619060.18719970.9690.9781000.2
4.369-4.7810.227910.18417570.18718480.9740.9781000.206
4.781-5.3390.23810.20615970.20716780.9640.9731000.233
5.339-6.1520.315670.23914330.24315000.9430.9641000.267
6.152-7.5030.321620.22912220.23412840.9460.9641000.259
7.503-10.4810.233560.2139760.21410320.9650.9731000.24
10.481-47.430.314420.3035990.3036410.9290.9381000.333

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