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- PDB-9oew: HalA N224V with lysine, succinate, chloride, and vanadium(IV)-oxo -

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Basic information

Entry
Database: PDB / ID: 9oew
TitleHalA N224V with lysine, succinate, chloride, and vanadium(IV)-oxo
ComponentsLysine halogenase
KeywordsBIOSYNTHETIC PROTEIN / Halogenase / Fe/2OG oxidase
Function / homology: / Halogenase D / LYSINE / SUCCINIC ACID / VANADIUM ION / oxovanadium(2+) / ArpA protein
Function and homology information
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKissman, E.N. / Stone, E.A. / Chang, M.C.Y.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DOE/LBL DEAC02-05CH11231 FWP CH030201 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134271 United States
CitationJournal: To Be Published
Title: Dynamic metal coordination controls chemoselectivity in a radical halogenase
Authors: Kissman, E.N. / Kipouros, I. / Slater, J.W. / Stone, E.A. / Yang, A.Y. / Braun, A. / Ensberg, A.R. / Whitten, A.M. / Chatterjee, K. / Bogacz, I. / Yano, J. / Bollinger Jr, J.M. / Chang, M.C.Y.
History
DepositionApr 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine halogenase
B: Lysine halogenase
C: Lysine halogenase
D: Lysine halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,62420
Polymers119,2024
Non-polymers1,42316
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Dimer of dimers in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.557, 146.557, 287.265
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-448-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Lysine halogenase


Mass: 29800.438 Da / Num. of mol.: 4 / Mutation: N224V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: FHX34_1011265 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A561WR11

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Non-polymers , 6 types, 162 molecules

#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: OV / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-V / VANADIUM ION


Mass: 50.941 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: V / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: HalA N224V crystals were obtained by the hanging drop vapor diffusion method by combining equal volumes of protein solution (HalA N224V (5 mg/ml), lysine (50 mM, pH 7), sodium succinate (20 ...Details: HalA N224V crystals were obtained by the hanging drop vapor diffusion method by combining equal volumes of protein solution (HalA N224V (5 mg/ml), lysine (50 mM, pH 7), sodium succinate (20 mM, pH 7), sodium chloride (100 mM) and vanadium(IV) oxide sulfate hydrate (1 mM)) and reservoir solution (potassium phosphate monobasic (40 mM), 20% (w/v) PEG 8000, 15% (v/v) glycerol)

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.4→116.1 Å / Num. obs: 46440 / % possible obs: 99.6 % / Redundancy: 20.04 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.358 / Rpim(I) all: 0.117 / Rrim(I) all: 0.376 / Net I/σ(I): 12.9
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 21.09 % / Rmerge(I) obs: 4.181 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 4549 / CC1/2: 0.802 / CC star: 0.944 / Rpim(I) all: 0.9232 / Rrim(I) all: 4.283 / % possible all: 99.02

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PDB_EXTRACT4.3data extraction
XDSJune 1, 2017data reduction
Aimless0.7.9data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→95.11 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 2445 5.27 %
Rwork0.2306 --
obs0.2333 46430 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→95.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7483 0 81 146 7710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037747
X-RAY DIFFRACTIONf_angle_d0.55810569
X-RAY DIFFRACTIONf_dihedral_angle_d14.7922646
X-RAY DIFFRACTIONf_chiral_restr0.0411221
X-RAY DIFFRACTIONf_plane_restr0.0051369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.450.40581400.33142521X-RAY DIFFRACTION99
2.45-2.50.36291160.31892596X-RAY DIFFRACTION99
2.5-2.560.38381400.30422555X-RAY DIFFRACTION99
2.56-2.620.38281410.2912546X-RAY DIFFRACTION99
2.62-2.70.33661520.28532536X-RAY DIFFRACTION100
2.7-2.770.36561350.28492584X-RAY DIFFRACTION99
2.77-2.860.34641290.29692587X-RAY DIFFRACTION99
2.86-2.970.33331290.26942577X-RAY DIFFRACTION99
2.97-3.090.27661580.25582560X-RAY DIFFRACTION100
3.09-3.230.28661440.2392577X-RAY DIFFRACTION100
3.23-3.40.31361430.23542578X-RAY DIFFRACTION100
3.4-3.610.29381560.22822582X-RAY DIFFRACTION100
3.61-3.890.25781350.20532617X-RAY DIFFRACTION100
3.89-4.280.26621600.18752585X-RAY DIFFRACTION100
4.28-4.90.22261430.17732622X-RAY DIFFRACTION100
4.9-6.170.26361560.21082632X-RAY DIFFRACTION100
6.17-95.110.22781680.21712730X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 22.7385 Å / Origin y: 41.6992 Å / Origin z: 24.1633 Å
111213212223313233
T0.2133 Å2-0.0175 Å20.0101 Å2-0.1125 Å2-0.0367 Å2--0.2614 Å2
L0.3639 °20.1031 °2-0.407 °2-0.3912 °2-0.335 °2--3.1357 °2
S-0.0456 Å °0.0164 Å °-0.0341 Å °-0.0559 Å °0.0765 Å °-0.0015 Å °0.4296 Å °-0.1561 Å °-0.0182 Å °
Refinement TLS groupSelection details: all

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