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- PDB-9pcn: Crystal structure of Rv0097 with vanadyl and CADA bound -

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Basic information

Entry
Database: PDB / ID: 9pcn
TitleCrystal structure of Rv0097 with vanadyl and CADA bound
Components(3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase
KeywordsOXIDOREDUCTASE / non-heme iron enzyme / Fe(II)/alpha-ketoglutarate-dependent dioxygenases / isonitrile synthase
Function / homology
Function and homology information


(R)-3-[(carboxymethyl)amino]fatty acid dioxygenase/decarboxylase / dioxygenase activity / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / oxovanadium(2+) / : / (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsYe, N. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
Citation
Journal: Nat Commun / Year: 2026
Title: A highly dynamic mononuclear non-heme iron enzyme for the two-step isonitrile biosynthesis.
Authors: Ye, N. / Del Rio Flores, A. / Zhang, W. / Drennan, C.L.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase
B: (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,37910
Polymers68,4242
Non-polymers9558
Water15,205844
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-10 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.274, 63.791, 91.015
Angle α, β, γ (deg.)90.000, 97.133, 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, 2 molecules AB

#1: Protein (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase


Mass: 34211.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0097, MTCY251.16 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WG83, (R)-3-[(carboxymethyl)amino]fatty acid dioxygenase/decarboxylase

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Non-polymers , 5 types, 852 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#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: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: OV / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 844 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 270 mM magnesium acetate, 16% w/v PEG 3350

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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: Nov 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.36→50 Å / Num. obs: 136943 / % possible obs: 97.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.24 Å2 / CC1/2: 0.999 / Net I/σ(I): 23.7
Reflection shellResolution: 1.36→1.44 Å / Num. unique obs: 20972 / CC1/2: 0.948

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→45.61 Å / SU ML: 0.1261 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.7034
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1837 6873 5.02 %
Rwork0.1631 130062 -
obs0.1642 136935 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.37 Å2
Refinement stepCycle: LAST / Resolution: 1.36→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4624 0 60 844 5528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00495025
X-RAY DIFFRACTIONf_angle_d0.83166866
X-RAY DIFFRACTIONf_chiral_restr0.0832747
X-RAY DIFFRACTIONf_plane_restr0.0088897
X-RAY DIFFRACTIONf_dihedral_angle_d12.44941918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.370.24531750.21933675X-RAY DIFFRACTION83.05
1.37-1.390.24712320.21433986X-RAY DIFFRACTION90.07
1.39-1.410.22842280.20044235X-RAY DIFFRACTION96.1
1.41-1.420.22531980.1924339X-RAY DIFFRACTION97.36
1.42-1.440.20032380.18784366X-RAY DIFFRACTION98.67
1.44-1.460.23412400.19934325X-RAY DIFFRACTION98.38
1.46-1.480.24192410.20484341X-RAY DIFFRACTION98.07
1.48-1.510.22222340.1914370X-RAY DIFFRACTION99.14
1.51-1.530.20012410.17774319X-RAY DIFFRACTION98.28
1.53-1.550.1892300.16924333X-RAY DIFFRACTION97.31
1.55-1.580.18312130.16774259X-RAY DIFFRACTION96.01
1.58-1.610.17912130.15964393X-RAY DIFFRACTION98.69
1.61-1.640.18362400.15864384X-RAY DIFFRACTION98.82
1.64-1.670.18012250.15734375X-RAY DIFFRACTION99.01
1.67-1.710.1652380.15954388X-RAY DIFFRACTION98.89
1.71-1.750.19052270.16394375X-RAY DIFFRACTION98.78
1.75-1.790.18692270.17414362X-RAY DIFFRACTION98.65
1.79-1.840.18822490.17884332X-RAY DIFFRACTION97.74
1.84-1.90.20362380.17654276X-RAY DIFFRACTION96.41
1.9-1.960.18922070.16424403X-RAY DIFFRACTION98.72
1.96-2.030.19932230.16834415X-RAY DIFFRACTION99.42
2.03-2.110.19362380.16544391X-RAY DIFFRACTION98.95
2.11-2.20.19312230.16224450X-RAY DIFFRACTION99.15
2.2-2.320.1812290.16144376X-RAY DIFFRACTION98.5
2.32-2.470.17422370.16474324X-RAY DIFFRACTION97.13
2.47-2.660.18912450.16364432X-RAY DIFFRACTION99.66
2.66-2.920.18052340.16584451X-RAY DIFFRACTION99.53
2.92-3.350.16792380.16194433X-RAY DIFFRACTION98.86
3.35-4.220.16792300.14384410X-RAY DIFFRACTION98.12
4.22-45.610.16032420.14094544X-RAY DIFFRACTION99.03

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