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- PDB-9n8s: Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjuga... -

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Basic information

Entry
Database: PDB / ID: 9n8s
TitleGlutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjugate at 2.03 Angstrom resolution
ComponentsGlutarate 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
: / Glutarate 2-hydroxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsHan, Z. / Mirkin, C.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-2428112 United States
Other governmentAir Force Office of Scientific Research FA9550-22-1-0300
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

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Assembly

Deposited unit
A: Glutarate 2-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4393
Polymers37,2871
Non-polymers1522
Water3,441191
1
A: Glutarate 2-hydroxylase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)299,51324
Polymers298,2988
Non-polymers1,21516
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)96.769, 96.769, 184.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

21A-614-

HOH

31A-668-

HOH

41A-673-

HOH

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Components

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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.05 M Bis-Tris pH 7, 1.5 M Lithium 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: 2.03→34.43 Å / Num. obs: 28337 / % possible obs: 98.8 % / Redundancy: 26.1 % / CC1/2: 0.781 / Rmerge(I) obs: 0.314 / Rpim(I) all: 0.088 / Rrim(I) all: 0.326 / Net I/σ(I): 10
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 20 % / Rmerge(I) obs: 2.838 / Num. unique obs: 2044 / CC1/2: 0.988 / Rpim(I) all: 0.904 / Rrim(I) all: 2.99 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDS20241002data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→34.43 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24365 1396 4.9 %RANDOM
Rwork0.20973 ---
obs0.21142 26934 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.758 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0 Å2
2---0.17 Å2-0 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 2.03→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 6 191 2572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122440
X-RAY DIFFRACTIONr_bond_other_d00.0162296
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.8353306
X-RAY DIFFRACTIONr_angle_other_deg0.7191.7665264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.382520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64510412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1190.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022900
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02600
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.992.9591161
X-RAY DIFFRACTIONr_mcbond_other2.9852.961161
X-RAY DIFFRACTIONr_mcangle_it4.3725.2751446
X-RAY DIFFRACTIONr_mcangle_other4.3715.2781447
X-RAY DIFFRACTIONr_scbond_it4.4373.3381279
X-RAY DIFFRACTIONr_scbond_other4.443.3381275
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2425.9421855
X-RAY DIFFRACTIONr_long_range_B_refined8.35228.942697
X-RAY DIFFRACTIONr_long_range_B_other8.31728.492653
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 85 -
Rwork0.345 1950 -
obs--97.32 %

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