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- PDB-9oet: Hydrox with succinate and vanadium(IV)-oxo -

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Basic information

Entry
Database: PDB / ID: 9oet
TitleHydrox with succinate and vanadium(IV)-oxo
ComponentsLysine hydroxylase
KeywordsBIOSYNTHETIC PROTEIN / Halogenase / Fe/2OG oxidase
Function / homology: / Halogenase D / metal ion binding / SUCCINIC ACID / oxovanadium(2+) / Lysine hydroxylase
Function and homology information
Biological speciesStreptomyces roseifaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKissman, E.N. / Yang, A.Y. / Whitten, A.M. / 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
D: Lysine hydroxylase
A: Lysine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8255
Polymers59,5732
Non-polymers2523
Water7,656425
1
D: Lysine hydroxylase
A: Lysine hydroxylase
hetero molecules

D: Lysine hydroxylase
A: Lysine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,64910
Polymers119,1464
Non-polymers5046
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)88.892, 139.970, 95.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-618-

HOH

21A-562-

HOH

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Components

#1: Protein Lysine hydroxylase


Mass: 29786.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces roseifaciens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8M0FGT0
#2: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: OV / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Hydrox crystals were obtained by the hanging drop vapor diffusion method by combining equal volumes of protein solution (Hydrox (5 mg/ml), lysine (50 mM, pH 7), sodium succinate (20 mM, pH 7) ...Details: Hydrox crystals were obtained by the hanging drop vapor diffusion method by combining equal volumes of protein solution (Hydrox (5 mg/ml), lysine (50 mM, pH 7), sodium succinate (20 mM, pH 7), and vanadium(IV) oxide sulfate hydrate (1 mM)) and reservoir solution (HEPES (100 mM), 16% (w/v) PEG 6000, magnesium chloride hexahydrate (200 mM), pH 9). 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 (Hydrox (5 mg/ml), lysine (50 mM, pH 7), sodium succinate (20 mM, pH 7), and vanadium(IV) oxide sulfate hydrate (1 mM)) and reservoir solution (HEPES (100 mM), 16% (w/v) PEG 6000, magnesium chloride hexahydrate (200 mM), pH 9)

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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: Aug 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.9→95.39 Å / Num. obs: 47209 / % possible obs: 100 % / Redundancy: 33.24 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.04 / Rrim(I) all: 0.168 / Net I/σ(I): 18.6
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 33.73 % / Rmerge(I) obs: 2.968 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 4669 / CC1/2: 0.773 / CC star: 0.934 / Rpim(I) all: 0.5123 / Rrim(I) all: 3.012 / % possible all: 99.62

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT4.3data extraction
XDSJune 1, 2017data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→75.04 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 2424 5.14 %
Rwork0.201 --
obs0.2032 47179 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→75.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 12 425 3804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073496
X-RAY DIFFRACTIONf_angle_d0.8934778
X-RAY DIFFRACTIONf_dihedral_angle_d14.3211206
X-RAY DIFFRACTIONf_chiral_restr0.056566
X-RAY DIFFRACTIONf_plane_restr0.015617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.32391350.29492608X-RAY DIFFRACTION99
1.94-1.980.29461490.26792616X-RAY DIFFRACTION100
1.98-2.030.27131260.23942600X-RAY DIFFRACTION100
2.03-2.080.26611480.22622607X-RAY DIFFRACTION100
2.08-2.130.28491480.23192590X-RAY DIFFRACTION100
2.13-2.20.27131370.22992601X-RAY DIFFRACTION100
2.2-2.270.2861290.22262611X-RAY DIFFRACTION100
2.27-2.350.2631310.20652629X-RAY DIFFRACTION100
2.35-2.440.24971340.21152635X-RAY DIFFRACTION100
2.44-2.550.24721510.2112602X-RAY DIFFRACTION100
2.55-2.690.2571610.2072622X-RAY DIFFRACTION100
2.69-2.860.27261430.2062624X-RAY DIFFRACTION100
2.86-3.080.22811650.2022616X-RAY DIFFRACTION100
3.08-3.390.22621360.18762629X-RAY DIFFRACTION100
3.39-3.880.23641340.18312685X-RAY DIFFRACTION100
3.88-4.880.20161240.16522711X-RAY DIFFRACTION100
4.89-75.040.23841730.21212769X-RAY DIFFRACTION100

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