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- PDB-9oer: HalA with lysine, Fe(II), chloride, and a peroxyhemiketal intermediate -

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Basic information

Entry
Database: PDB / ID: 9oer
TitleHalA with lysine, Fe(II), chloride, and a peroxyhemiketal intermediate
ComponentsLysine halogenase
KeywordsBIOSYNTHETIC PROTEIN / Halogenase / Fe/2OG oxidase
Function / homology: / Halogenase D / : / 2-OXOGLUTARIC ACID / : / LYSINE / SUCCINIC ACID / : / ArpA protein
Function and homology information
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsKissman, E.N. / Yang, A.Y. / 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: Nat.Chem.Biol. / Year: 2025
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. / Martin Bollinger Jr., J. / Chang, M.C.Y.
History
DepositionApr 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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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)241,59440
Polymers238,5238
Non-polymers3,07132
Water12,556697
1
A: Lysine halogenase
B: Lysine halogenase
G: Lysine halogenase
H: Lysine halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,74920
Polymers119,2624
Non-polymers1,48816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lysine halogenase
D: Lysine halogenase
E: Lysine halogenase
F: Lysine halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,84520
Polymers119,2624
Non-polymers1,58316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.300, 147.300, 287.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11G-473-

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, 729 molecules

#2: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-YL0 / (4R)-4-chloro-L-lysine


Mass: 180.633 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13ClN2O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-A1CA1 / (2S)-2-hydroperoxy-2-hydroxypentanedioic acid


Mass: 180.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O7 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HalA crystals were obtained by the hanging drop vapor diffusion method by combining equal volumes of protein solution (HalA (5 mg/ml), lysine (50 mM, pH 7), and aKG (20 mM, pH 7)) and ...Details: HalA crystals were obtained by the hanging drop vapor diffusion method by combining equal volumes of protein solution (HalA (5 mg/ml), lysine (50 mM, pH 7), and aKG (20 mM, pH 7)) and reservoir solution (potassium phosphate monobasic (40 mM), 20% (w/v) PEG 8000, 15% (v/v) glycerol). Crystals grew in three days and were transferred to an Eppendorf tube containing 250 uL of reservoir solution and vortexed for 30 seconds with 10 x 1 uM diameter zirconia/silica beads to produce a micro-seed solution. The seed solution was stored at -80C for future use. Subsequent crystals were prepared by micro-seeding equal volumes of protein solution (HalA (5 mg/ml), lysine (50 mM, pH 7), and aKG (20 mM, pH 7)) and reservoir solution (potassium phosphate monobasic (40 mM), 20% (w/v) PEG 8000, 15% (v/v) glycerol). Crystals grew after two weeks inside a Coy anaerobic chamber. Crystals were soaked with (NH4)2Fe(SO4)2 6H2O (1.42 mM) while NO accumulated in the well. To introduce NO, diethylamine NONOate was prepared by dissolving solid in 10 mM NaOH. The stock concentration was determined based on the published extinction coefficient of e250 = 6,500 M-1 cm-1 using a Nanodrop. NONOate was added to a final concentration of 26 mM in each well along with 150 mM HEPES pH 7.5 to trigger NONOate decomposition. The wells were quickly re-sealed and NO was allowed to accumulate for approximately 1 hour, after which the crystals were flash frozen in liquid nitrogen

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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 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.46
ReflectionResolution: 1.72→95.96 Å / Num. obs: 246753 / % possible obs: 99.7 % / Redundancy: 38.94 % / CC1/2: 0.996 / CC star: 1 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.041 / Rrim(I) all: 0.186 / Net I/σ(I): 19.5
Reflection shellResolution: 1.72→1.781 Å / Redundancy: 26.67 % / Rmerge(I) obs: 2.376 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 24600 / CC1/2: 0.657 / CC star: 0.89 / Rpim(I) all: 0.4643 / Rrim(I) all: 2.422 / % possible all: 99.13

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSJune 1, 2017data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PDB_EXTRACT4.3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→95.96 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.58 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2012 12540 5.08 %
Rwork0.1684 --
obs0.1784 246749 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→95.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15552 0 171 697 16420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d0.678
X-RAY DIFFRACTIONf_dihedral_angle_d12.3915647
X-RAY DIFFRACTIONf_chiral_restr0.0422499
X-RAY DIFFRACTIONf_plane_restr0.0092827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.750.33446540.298411682X-RAY DIFFRACTION94
1.75-1.780.31086440.27511620X-RAY DIFFRACTION94
1.78-1.820.27595740.261411650X-RAY DIFFRACTION95
1.82-1.850.28365590.249711727X-RAY DIFFRACTION95
1.85-1.890.25936850.230611634X-RAY DIFFRACTION94
1.89-1.940.30556020.262511696X-RAY DIFFRACTION95
1.94-1.990.22016440.213111705X-RAY DIFFRACTION94
1.99-2.040.21426250.204411739X-RAY DIFFRACTION95
2.04-2.10.22586390.202311700X-RAY DIFFRACTION95
2.1-2.170.20836130.194611727X-RAY DIFFRACTION95
2.17-2.240.24066060.202511770X-RAY DIFFRACTION95
2.24-2.330.22066520.19111660X-RAY DIFFRACTION94
2.33-2.440.21375940.186611725X-RAY DIFFRACTION95
2.44-2.570.22456370.187811777X-RAY DIFFRACTION95
2.57-2.730.20845790.180711785X-RAY DIFFRACTION95
2.73-2.940.21446110.176911752X-RAY DIFFRACTION95
2.94-3.240.19946590.165911669X-RAY DIFFRACTION95
3.24-3.710.20146360.154511766X-RAY DIFFRACTION95
3.71-4.670.17296690.134611692X-RAY DIFFRACTION95
4.67-95.960.18586540.151811737X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 26.2442 Å / Origin y: 42.5742 Å / Origin z: -33.5577 Å
111213212223313233
T0.2335 Å2-0.0134 Å2-0.0042 Å2-0.228 Å2-0.0021 Å2--0.1235 Å2
L0.1506 °2-0.0016 °2-0.0685 °2-0.1273 °2-0.0787 °2--0.4858 °2
S0.0272 Å °-0.015 Å °0.0195 Å °0.0056 Å °-0.006 Å °-0.0049 Å °-0.033 Å °0.0083 Å °-0.021 Å °
Refinement TLS groupSelection details: all

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