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- PDB-9n8u: Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjuga... -

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Basic information

Entry
Database: PDB / ID: 9n8u
TitleGlutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjugate at 1.74 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: 1.74 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
F: DNA (5'-P*AP*GP*CP*T-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5397
Polymers36,0512
Non-polymers4875
Water2,864159
1
A: Glutarate 2-hydroxylase
F: DNA (5'-P*AP*GP*CP*T-3')
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)292,30956
Polymers288,41216
Non-polymers3,89740
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)96.648, 96.648, 184.208
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-599-

HOH

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Components

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Protein / DNA chain , 2 types, 2 molecules AF

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


Mass: 34860.664 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, 164 molecules

#3: 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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-A1BWE / 1-(2-hydroxyethyl)pyrrolidine-2,5-dione


Mass: 143.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 55.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 25 % v/v Glycerol, 0.05 M Bis-Tris pH 7, 1.4 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: 1.74→34.17 Å / Num. obs: 45057 / % possible obs: 100 % / Redundancy: 27 % / CC1/2: 1 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.048 / Rrim(I) all: 0.182 / Net I/σ(I): 18.9
Reflection shellResolution: 1.74→1.77 Å / Rmerge(I) obs: 2.499 / Num. unique obs: 2429 / CC1/2: 0.328 / Rpim(I) all: 0.69 / Rrim(I) all: 2.593

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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: 1.74→34.17 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.166 / Average fsc free: 0.9539 / Average fsc work: 0.9608 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.1 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 2314 5.136 %RANDOM
Rwork0.2039 42742 --
all0.205 ---
obs-45056 99.971 %-
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: 35.218 Å2
Baniso -1Baniso -2Baniso -3
1--0.278 Å20 Å20 Å2
2---0.278 Å20 Å2
3---0.556 Å2
Refinement stepCycle: LAST / Resolution: 1.74→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 82 26 159 2638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122547
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.8253464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2525287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.132520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54910412
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.65410127
X-RAY DIFFRACTIONr_chiral_restr0.1310.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021937
X-RAY DIFFRACTIONr_nbd_refined0.1990.21128
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21723
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2181
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2160.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.28
X-RAY DIFFRACTIONr_mcbond_it3.2082.8061157
X-RAY DIFFRACTIONr_mcangle_it4.4655.0031441
X-RAY DIFFRACTIONr_scbond_it5.6154.1311390
X-RAY DIFFRACTIONr_scangle_it7.6897.3922023
X-RAY DIFFRACTIONr_lrange_it10.8739.8333932
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
1.74-1.7850.3371670.34131160.34132830.9230.9121000.33
1.785-1.8340.3171740.3130020.31131760.9280.9281000.294
1.834-1.8870.31600.29429550.29431150.9280.9341000.272
1.887-1.9450.3051590.26528680.26730270.930.9491000.24
1.945-2.0080.2651380.2427970.24129350.950.9581000.208
2.008-2.0790.261480.21926800.22128280.9540.9671000.186
2.079-2.1570.2261390.21326050.21327440.9650.9681000.179
2.157-2.2440.2771400.21225090.21626490.9540.971000.175
2.244-2.3440.2461420.20723960.20925380.9620.9731000.169
2.344-2.4580.221150.20723070.20724220.9670.9741000.17
2.458-2.590.2321070.20322210.20423280.9680.9751000.166
2.59-2.7460.2221080.20821080.20922160.9730.9751000.171
2.746-2.9340.2331040.21519750.21620790.9630.9711000.178
2.934-3.1670.2331060.20518270.20719330.9630.9731000.174
3.167-3.4670.199920.19217160.19218080.9730.9771000.166
3.467-3.8710.19890.17915470.1816360.9740.9821000.16
3.871-4.460.176710.14513800.14614520.9820.98999.93110.134
4.46-5.4390.159750.15411840.15412590.9820.9871000.144
5.439-7.5970.256490.2099520.21210010.9620.9731000.193
7.597-34.170.232310.185970.1826280.9680.9771000.164

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