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- PDB-9n8v: Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjuga... -

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Basic information

Entry
Database: PDB / ID: 9n8v
TitleGlutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjugate at 1.78 Angstrom resolution
Components
  • DNA (5'-P*AP*GP*CP*T-3')
  • Glutarate 2-hydroxylase
KeywordsMETAL BINDING PROTEIN / Oxygenase / Hydroxylase / Metal binding
Function / homology
Function and homology information


glutarate dioxygenase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with 2-oxoglutarate as one donor, and the other dehydrogenated / glutarate dioxygenase activity / L-lysine catabolic process / ferrous iron binding
Similarity search - Function
Glutarate 2-hydroxylase GlaH / CsiD / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
: / DNA / Glutarate 2-hydroxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsHan, Z. / Mirkin, C.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-2428112 United States
Other governmentFA9550-22-1-0300 United States
CitationJournal: Sci Adv / Year: 2026
Title: Diffraction-quality, ultraflexible protein single crystals engineered with DNA.
Authors: Han, Z. / Mirkin, C.A.
History
DepositionFeb 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutarate 2-hydroxylase
E: DNA (5'-P*AP*GP*CP*T-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9107
Polymers38,4782
Non-polymers4325
Water3,081171
1
A: Glutarate 2-hydroxylase
E: DNA (5'-P*AP*GP*CP*T-3')
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)311,28256
Polymers307,82516
Non-polymers3,45740
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2_555-x,-y,z1
point symmetry operation3_555-y,x,z1
point symmetry operation4_555y,-x,z1
point symmetry operation5_555-x,y,-z1
point symmetry operation6_555x,-y,-z1
point symmetry operation7_555y,x,-z1
point symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)96.524, 96.524, 184.354
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-596-

HOH

21A-614-

HOH

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Components

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Protein / DNA chain , 2 types, 2 molecules AE

#1: Protein Glutarate 2-hydroxylase / G-2-H


Mass: 37287.254 Da / Num. of mol.: 1 / Mutation: Q184C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glaH, EcolC_1047 / Production host: Escherichia coli (E. coli) / References: UniProt: B1IVJ9, glutarate dioxygenase
#2: DNA chain DNA (5'-P*AP*GP*CP*T-3')


Mass: 1190.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 176 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Potassium chloride, 25 % v/v Glycerol, 0.05 M Bis-Tris pH 7, 1.6 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920194 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920194 Å / Relative weight: 1
ReflectionResolution: 1.78→34.13 Å / Num. obs: 42058 / % possible obs: 100 % / Redundancy: 27.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.052 / Rrim(I) all: 0.196 / Net I/σ(I): 15.9
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 26.5 % / Rmerge(I) obs: 2.749 / Num. unique obs: 2371 / CC1/2: 0.334 / Rpim(I) all: 0.768 / Rrim(I) all: 2.854 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.128)refinement
XDS20241002data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→34.126 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.104 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 2099 4.992 %RANDOM
Rwork0.2017 39952 --
all0.203 ---
obs-42051 99.948 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.808 Å2
Baniso -1Baniso -2Baniso -3
1--0.444 Å20 Å20 Å2
2---0.444 Å20 Å2
3---0.888 Å2
Refinement stepCycle: LAST / Resolution: 1.78→34.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 82 23 171 2607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122518
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.8233425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.065519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76510410
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.99710124
X-RAY DIFFRACTIONr_chiral_restr0.1240.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021905
X-RAY DIFFRACTIONr_nbd_refined0.2010.21129
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21678
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2175
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.27
X-RAY DIFFRACTIONr_mcbond_it3.2352.8721151
X-RAY DIFFRACTIONr_mcangle_it4.5865.1191437
X-RAY DIFFRACTIONr_scbond_it5.3134.121367
X-RAY DIFFRACTIONr_scangle_it7.7637.4231988
X-RAY DIFFRACTIONr_lrange_it9.49541.3113876
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.78-1.8260.3711450.33729190.33830640.8940.9191000.328
1.826-1.8760.3451560.31428180.31529750.9040.92699.96640.301
1.876-1.930.3111430.28627470.28828900.9330.9371000.267
1.93-1.9890.3041330.26726770.26928100.9370.9491000.242
1.989-2.0540.2751400.23926090.24127500.9450.95899.96360.211
2.054-2.1260.251230.22525160.22626390.9590.9641000.197
2.126-2.2060.2811350.21224490.21525850.9480.96899.96130.181
2.206-2.2960.249990.21823570.2224560.9620.9681000.182
2.296-2.3980.2791380.20822260.21223640.9530.9721000.172
2.398-2.5140.2341110.20621550.20722660.9640.9741000.169
2.514-2.6490.2711160.2120450.21421610.9620.9731000.175
2.649-2.8090.2081160.20619480.20620660.9720.97599.90320.172
2.809-3.0010.191930.20918530.20819460.9780.9731000.175
3.001-3.240.202900.19517230.19618140.9750.97699.94490.17
3.24-3.5460.226870.18915840.19116720.9690.97899.94020.168
3.546-3.9590.215830.17514560.17715400.970.98299.93510.16
3.959-4.5610.145710.14912890.14813610.9890.98899.92650.14
4.561-5.5610.177510.14211210.14311730.9830.98999.91470.135
5.561-7.7620.203390.1878990.1889380.9770.9791000.177
7.762-34.1260.141300.1915610.1885910.990.9751000.181

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