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- PDB-9pay: Crystal structure of Rv0097 F102W variant with vanadyl and CADA bound -

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Basic information

Entry
Database: PDB / ID: 9pay
TitleCrystal structure of Rv0097 F102W variant 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 / oxovanadium(2+) / : / (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 25, 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)69,1867
Polymers68,5022
Non-polymers6845
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-14 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.848, 62.075, 90.918
Angle α, β, γ (deg.)90.000, 94.524, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 30 or resid 33...
d_2ens_1(chain "B" and (resid 3 through 30 or resid 33...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUILEILEAA3 - 303 - 30
d_12ILEILEVALVALAA33 - 8033 - 80
d_13SERSERILEILEAA82 - 17582 - 175
d_14THRTHRLYSLYSAA179 - 290179 - 290
d_15VY9VY9VY9VY9AC401
d_16VVOVVOVVOVVOAD402
d_21LEULEUILEILEBB3 - 303 - 30
d_22ILEILEVALVALBB33 - 8033 - 80
d_23SERSERILEILEBB81 - 17581 - 175
d_24THRTHRGLYGLYBB178 - 265178 - 265
d_25GLYGLYLYSLYSBB269 - 290269 - 290
d_26VY9VY9VY9VY9BF402
d_27VVOVVOVVOVVOBG403

NCS oper: (Code: givenMatrix: (0.98714757903, 0.00114908090455, 0.159807186411), (0.00116922600638, -0.999999315942, -3.20292418597E-5), (0.15980704029, 0.000218468306918, -0.987148247299)Vector: -3. ...NCS oper: (Code: given
Matrix: (0.98714757903, 0.00114908090455, 0.159807186411), (0.00116922600638, -0.999999315942, -3.20292418597E-5), (0.15980704029, 0.000218468306918, -0.987148247299)
Vector: -3.68262583962, -4.17517105871, 45.3188325953)

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Components

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


Mass: 34251.016 Da / Num. of mol.: 2 / Mutation: F102W
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
#2: 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
#3: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: OV / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
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: Jun 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 42517 / % possible obs: 97.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 32.32 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.12 Å / Num. unique obs: 6687 / CC1/2: 0.87

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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: 2→42.25 Å / SU ML: 0.2501 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9839
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2419 2138 5.03 %
Rwork0.194 40367 -
obs0.1963 42505 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.07 Å2
Refinement stepCycle: LAST / Resolution: 2→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 42 267 4903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00524814
X-RAY DIFFRACTIONf_angle_d0.75116564
X-RAY DIFFRACTIONf_chiral_restr0.0538715
X-RAY DIFFRACTIONf_plane_restr0.0073850
X-RAY DIFFRACTIONf_dihedral_angle_d12.54861813
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.51586538823 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.33271350.27172588X-RAY DIFFRACTION94.38
2.05-2.10.36631450.26272571X-RAY DIFFRACTION95.4
2.1-2.160.26991340.2292716X-RAY DIFFRACTION98.07
2.16-2.220.24511420.21942719X-RAY DIFFRACTION98.35
2.22-2.290.28331320.22642712X-RAY DIFFRACTION98.65
2.29-2.370.30061500.22212673X-RAY DIFFRACTION98.5
2.37-2.470.24491460.21652665X-RAY DIFFRACTION97.2
2.47-2.580.28031470.23062621X-RAY DIFFRACTION95.68
2.58-2.720.26631400.22652702X-RAY DIFFRACTION98.61
2.72-2.890.28151360.21962737X-RAY DIFFRACTION98.19
2.89-3.110.28531550.22362703X-RAY DIFFRACTION98.72
3.11-3.420.25161370.20772679X-RAY DIFFRACTION96.8
3.42-3.920.22631510.18552741X-RAY DIFFRACTION99.21
3.92-4.930.1821400.13992721X-RAY DIFFRACTION97.51
4.93-42.250.19421480.1592819X-RAY DIFFRACTION98.87

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