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

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Basic information

Entry
Database: PDB / ID: 8evn
TitleSulfatase from Mycobacterium tuberculosis (Rv3406) in complex with N-oxalylglycine (NOG)
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 / N-OXALYLGLYCINE / Alpha-ketoglutarate-dependent sulfate ester dioxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.644 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)132,55013
Polymers131,6054
Non-polymers9459
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-74 kcal/mol
Surface area35630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.535, 128.336, 138.693
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-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
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: 100 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: Mar 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.64→47.676 Å / Num. obs: 34771 / % possible obs: 99.2 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rpim(I) all: 0.03 / Net I/σ(I): 11.9
Reflection shellResolution: 2.64→2.77 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4332 / CC1/2: 0.86 / Rpim(I) all: 0.381 / % possible all: 94.5

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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: 2.644→47.676 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 48.609 / SU ML: 0.422 / Cross valid method: FREE R-VALUE / ESU R: 0.944 / ESU R Free: 0.381
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2995 1734 5.006 %random selection
Rwork0.2502 32901 --
all0.253 ---
obs-34635 98.988 %-
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: 85.363 Å2
Baniso -1Baniso -2Baniso -3
1-13.329 Å20 Å2-0 Å2
2---6.662 Å20 Å2
3----6.667 Å2
Refinement stepCycle: LAST / Resolution: 2.644→47.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7227 0 52 13 7292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0127463
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166589
X-RAY DIFFRACTIONr_angle_refined_deg0.6411.63310161
X-RAY DIFFRACTIONr_angle_other_deg0.2411.55115230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4155931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.2211066
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.598101073
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.45410346
X-RAY DIFFRACTIONr_chiral_restr0.0290.21148
X-RAY DIFFRACTIONr_chiral_restr_other0.0210.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028695
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021529
X-RAY DIFFRACTIONr_nbd_refined0.1720.21377
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.26604
X-RAY DIFFRACTIONr_nbtor_refined0.1630.23555
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23990
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2162
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0840.23
X-RAY DIFFRACTIONr_nbd_other0.0920.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.21
X-RAY DIFFRACTIONr_mcbond_it0.7015.5243761
X-RAY DIFFRACTIONr_mcbond_other0.75.5233760
X-RAY DIFFRACTIONr_mcangle_it1.2128.2824679
X-RAY DIFFRACTIONr_mcangle_other1.2128.2824680
X-RAY DIFFRACTIONr_scbond_it1.2195.6243702
X-RAY DIFFRACTIONr_scbond_other1.2175.6243702
X-RAY DIFFRACTIONr_scangle_it1.1878.3895482
X-RAY DIFFRACTIONr_scangle_other1.1878.395483
X-RAY DIFFRACTIONr_lrange_it2.57865.6847913
X-RAY DIFFRACTIONr_lrange_other2.57865.697914
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
2.644-2.7130.52970.47320870.47525220.5810.71286.59790.471
2.713-2.7870.431310.41923500.4224810.7820.7421000.41
2.787-2.8670.431090.38923140.3924230.7680.7851000.372
2.867-2.9550.4251190.36922150.37123340.840.8171000.349
2.955-3.0520.3461310.34221420.34222730.8650.861000.314
3.052-3.1590.311140.29720900.29822040.9010.9131000.269
3.159-3.2770.3221130.27320410.27621540.9370.941000.248
3.277-3.410.3111050.24219170.24620220.9220.9591000.221
3.41-3.5610.282970.24518770.24619740.9490.9621000.223
3.561-3.7340.275820.22918070.23118900.9480.96699.94710.211
3.734-3.9350.23850.21417080.21517930.9670.9721000.194
3.935-4.1720.21720.19416500.19417220.9730.9771000.177
4.172-4.4570.23830.19515300.19716130.9670.9771000.186
4.457-4.8110.223680.1914400.19215080.9620.9771000.186
4.811-5.2650.284950.21812990.22213940.9560.9691000.213
5.265-5.8770.36660.26112210.26612870.9420.9561000.251
5.877-6.7690.38650.28510660.2911310.930.9511000.279
6.769-8.2490.358260.2459560.2489820.9060.9611000.253
8.249-11.4950.224450.1987320.1997770.9690.9761000.221
11.495-47.6760.347310.2844590.2884910.9260.93599.79630.298
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1301-0.68460.5344.3565-0.53391.69420.2101-0.0705-0.0750.02090.003-0.23670.47050.2208-0.2130.28390.0787-0.1960.3821-0.04190.155713.1773-9.771-11.6797
21.8651-0.88840.19243.373-0.00762.5837-0.1447-0.3943-0.12130.90910.28850.33110.0774-0.2859-0.14390.28970.06760.0520.4688-0.04620.08660.513.82865.525
31.1943-0.25670.94784.1857-1.35934.2457-0.0146-0.0787-0.2466-0.67440.34160.90520.3184-0.3486-0.3270.2011-0.1042-0.20520.38240.07510.2989-11.736617.5224-41.5417
41.0695-0.02180.65153.57090.11725.2348-0.21180.3720.1348-0.51340.1867-0.5843-0.31851.01480.02510.1272-0.16830.05870.6548-0.03330.147314.40632.3446-35.4628
Refinement TLS groupSelection: ALL

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