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- PDB-8kht: The structure of Rv0097 with substrate -

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Basic information

Entry
Database: PDB / ID: 8kht
TitleThe structure of Rv0097 with substrate
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / Rv0097 / Fe/2OG enzymes
Function / homology
Function and homology information


taurine dioxygenase / taurine dioxygenase activity / Oxidoreductases / metal ion binding
Similarity search - Function
: / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
: / : / Oxidoreductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChen, J. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0901900 China
CitationJournal: Acs Catalysis / Year: 2024
Title: Variation in biosynthesis and metal-binding properties of isonitrile-containing peptides produced by Mycobacteria versus Streptomyces.
Authors: Chen, T.Y. / Chen, J. / Ruszczycky, M.W. / Hilovsky, D. / Hostetler, T. / Liu, X. / Zhou, J. / Chang, W.C.
History
DepositionAug 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 16, 2025Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond / pdbx_entry_details
Item: _chem_comp_atom.pdbx_stereo_config / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.pdbx_stereo_config / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.value_order / _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: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5916
Polymers68,9882
Non-polymers6024
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-13 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.740, 89.070, 63.510
Angle α, β, γ (deg.)90.000, 90.026, 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

#1: Protein Oxidoreductase / Rv0097


Mass: 34494.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: tauD_2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A045GL20
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-VY9 / (3R)-3-(2-hydroxy-2-oxoethylamino)decanoic acid


Mass: 245.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H23NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris/HCl (pH 8.5), 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→63.51 Å / Num. obs: 39281 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 38.37 Å2 / CC1/2: 0.998 / Net I/σ(I): 17
Reflection shellResolution: 2.05→2.1 Å / Num. unique obs: 2822 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→28.37 Å / SU ML: 0.2861 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.4168 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2664 1845 4.77 %
Rwork0.2072 36828 -
obs0.2101 38673 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.04 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4558 0 36 208 4802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734754
X-RAY DIFFRACTIONf_angle_d0.94116477
X-RAY DIFFRACTIONf_chiral_restr0.058708
X-RAY DIFFRACTIONf_plane_restr0.0076838
X-RAY DIFFRACTIONf_dihedral_angle_d5.21353974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.41531020.40612657X-RAY DIFFRACTION90.88
2.11-2.170.38341630.30382865X-RAY DIFFRACTION99.54
2.17-2.240.37131570.2782766X-RAY DIFFRACTION96.31
2.24-2.320.3511170.30472617X-RAY DIFFRACTION90.56
2.32-2.410.33321390.25332908X-RAY DIFFRACTION99.67
2.41-2.520.32561510.23322855X-RAY DIFFRACTION99.87
2.52-2.650.3021710.23622879X-RAY DIFFRACTION99.58
2.65-2.820.33541540.24682831X-RAY DIFFRACTION98.09
2.82-3.040.30291470.23662920X-RAY DIFFRACTION99.77
3.04-3.340.2481310.21492899X-RAY DIFFRACTION99.34
3.34-3.820.27371240.20482838X-RAY DIFFRACTION97.72
3.82-4.810.20981290.15242912X-RAY DIFFRACTION98.45
4.81-28.370.20331600.15982881X-RAY DIFFRACTION97.56

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