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- PDB-9n8d: Glutarate L-2-hydroxylase N182A, Q184C mutant-5'-Mal-C2-AGCT DNA ... -

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Basic information

Entry
Database: PDB / ID: 9n8d
TitleGlutarate L-2-hydroxylase N182A, Q184C mutant-5'-Mal-C2-AGCT DNA conjugate
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: 1.84 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 8, 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
D: DNA (5'-P*AP*GP*CP*T-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8266
Polymers38,4352
Non-polymers3914
Water2,432135
1
A: Glutarate 2-hydroxylase
D: DNA (5'-P*AP*GP*CP*T-3')
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)310,60948
Polymers307,48016
Non-polymers3,12932
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)96.757, 96.757, 183.930
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-612-

HOH

21A-623-

HOH

31A-629-

HOH

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Components

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Protein / DNA chain , 2 types, 2 molecules AD

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


Mass: 37244.230 Da / Num. of mol.: 1 / Mutation: N182A, 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 / Details: final dT not modeled but present experimentally / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 139 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.: 2 / 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.: 135 / 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: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M Sodium cacodylate trihydrate pH 6.5, 2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 1.84→54.89 Å / Num. obs: 38003 / % possible obs: 99.6 % / Redundancy: 27.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.055 / Rrim(I) all: 0.208 / Net I/σ(I): 11.7
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 19.5 % / Rmerge(I) obs: 5.488 / Num. unique obs: 2205 / CC1/2: 0.356 / Rpim(I) all: 1.803 / Rrim(I) all: 5.789 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDS20240723data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→51.84 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23818 1913 5 %RANDOM
Rwork0.20672 ---
obs0.20832 36065 99.43 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.125 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0 Å2-0 Å2
2---0.75 Å2-0 Å2
3---1.5 Å2
Refinement stepCycle: 1 / Resolution: 1.84→51.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 62 21 135 2598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122540
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.8313447
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7265291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.123520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95610414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021939
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.3513.7381170
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.9336.6741459
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8625.1811370
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.89549.723785
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.841→1.889 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 128 -
Rwork0.358 2498 -
obs--94.84 %

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