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- PDB-9oes: HalA with lysine, succinate, chloride, and vanadium(IV)-oxo at pH 4.2 -

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Basic information

Entry
Database: PDB / ID: 9oes
TitleHalA with lysine, succinate, chloride, and vanadium(IV)-oxo at pH 4.2
ComponentsLysine halogenase
KeywordsBIOSYNTHETIC PROTEIN / Halogenase / Fe/2OG oxidase
Function / homology: / Halogenase D / CITRATE ANION / LYSINE / TRIETHYLENE GLYCOL / SUCCINIC ACID / VANADIUM ION / oxovanadium(2+) / ArpA protein
Function and homology information
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsKissman, E.N. / 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
E: Lysine halogenase
F: Lysine halogenase
G: Lysine halogenase
H: Lysine halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,48247
Polymers238,5238
Non-polymers3,95839
Water25,5451418
1
A: Lysine halogenase
C: Lysine halogenase
D: Lysine halogenase
H: Lysine halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,98522
Polymers119,2624
Non-polymers1,72318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine halogenase
E: Lysine halogenase
F: Lysine halogenase
G: Lysine halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,49725
Polymers119,2624
Non-polymers2,23521
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.950, 146.950, 287.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11H-523-

HOH

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Lysine halogenase


Mass: 29815.410 Da / Num. of mol.: 8
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 , 8 types, 1457 molecules

#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-VVO / oxovanadium(2+)


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


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#8: Chemical
ChemComp-V / VANADIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1418 / 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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: HalA crystals were obtained by the sitting drop vapor diffusion method by combining equal volumes of protein solution (HalA (15 mg/ml), lysine (50 mM, pH 7), sodium succinate (20 mM, pH 7), ...Details: HalA crystals were obtained by the sitting drop vapor diffusion method by combining equal volumes of protein solution (HalA (15 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, dissolved in 2.5 mM H2SO4)) and reservoir solution (sodium phosphate dibasic/citric acid (100 mM), 40% (w/v) PEG 300, pH 4.2)

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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 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.93→95.99 Å / Num. obs: 173594 / % possible obs: 99.6 % / Redundancy: 53.12 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.361 / Rpim(I) all: 0.07 / Rrim(I) all: 0.368 / Net I/σ(I): 13.5
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 24.77 % / Rmerge(I) obs: 5.306 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 201303 / CC1/2: 0.536 / Rpim(I) all: 1.517 / Rrim(I) all: 5.528 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
PDB_EXTRACT4.3data extraction
XDSFeb 5, 2021data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→95.35 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 8718 5.03 %
Rwork0.1745 --
obs0.1766 173238 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15845 0 237 1418 17500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716492
X-RAY DIFFRACTIONf_angle_d0.81322439
X-RAY DIFFRACTIONf_dihedral_angle_d14.8915904
X-RAY DIFFRACTIONf_chiral_restr0.052539
X-RAY DIFFRACTIONf_plane_restr0.0092912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.950.40082500.36965088X-RAY DIFFRACTION92
1.95-1.970.36462700.33615224X-RAY DIFFRACTION95
1.97-20.35032860.30235410X-RAY DIFFRACTION98
2-2.020.32862740.28475476X-RAY DIFFRACTION99
2.02-2.050.3233090.26115517X-RAY DIFFRACTION100
2.05-2.080.29972890.24915518X-RAY DIFFRACTION100
2.08-2.110.28353030.23125483X-RAY DIFFRACTION100
2.11-2.140.26763030.21835510X-RAY DIFFRACTION100
2.14-2.170.26153090.21055476X-RAY DIFFRACTION100
2.17-2.210.26243050.21155552X-RAY DIFFRACTION100
2.21-2.250.2973000.22775482X-RAY DIFFRACTION100
2.25-2.290.30232950.2175482X-RAY DIFFRACTION99
2.29-2.330.26162790.2025537X-RAY DIFFRACTION100
2.33-2.380.28442630.19625521X-RAY DIFFRACTION100
2.38-2.430.24973110.19025487X-RAY DIFFRACTION100
2.43-2.490.25972700.19055527X-RAY DIFFRACTION100
2.49-2.550.25042900.1815513X-RAY DIFFRACTION100
2.55-2.620.23232740.17615574X-RAY DIFFRACTION100
2.62-2.70.23723370.18065420X-RAY DIFFRACTION100
2.7-2.780.23523120.17545551X-RAY DIFFRACTION100
2.78-2.880.23843140.17725471X-RAY DIFFRACTION100
2.88-30.2082990.17395539X-RAY DIFFRACTION100
3-3.130.21862870.1695518X-RAY DIFFRACTION100
3.14-3.30.19742620.16665545X-RAY DIFFRACTION100
3.3-3.510.19572810.15875528X-RAY DIFFRACTION100
3.51-3.780.17412930.14415525X-RAY DIFFRACTION100
3.78-4.160.14752860.13235519X-RAY DIFFRACTION100
4.16-4.760.1642680.1235546X-RAY DIFFRACTION100
4.76-60.19023200.14785469X-RAY DIFFRACTION100
6-95.350.16052790.16445512X-RAY DIFFRACTION99

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