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- PDB-9n7p: Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjuga... -

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Basic information

Entry
Database: PDB / ID: 9n7p
TitleGlutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjugate at 1.89 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: 1.891 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 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4393
Polymers37,2871
Non-polymers1522
Water2,540141
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)97.043, 97.043, 185.372
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 37287.254 Da / Num. of mol.: 1
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.: 141 / 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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 10 % v/v Glycerol, 0.05 M MES pH 5.5, 1.5 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980099 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980099 Å / Relative weight: 1
ReflectionResolution: 1.89→48.52 Å / Num. obs: 35691 / % possible obs: 99.8 % / Redundancy: 26.4 % / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.022 / Rrim(I) all: 0.082 / Χ2: 1.01 / Net I/σ(I): 27.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.07-48.5219.80.0381.339010.0090.0310.7999.3
1.89-1.9325.91.4672.622080.7760.411.5240.9997.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Coot0.9.8.92model building
Aimless0.7.15data scaling
XDS20230630data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.891→48.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.001 / SU ML: 0.087 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.12 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2283 1758 4.926 %
Rwork0.2 33932 -
all0.201 --
obs-35690 99.807 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.192 Å2
Baniso -1Baniso -2Baniso -3
1--0.339 Å20 Å2-0 Å2
2---0.339 Å2-0 Å2
3---0.678 Å2
Refinement stepCycle: LAST / Resolution: 1.891→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 0 6 141 2512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122437
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.8353303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9135288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.713520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21110413
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.15610127
X-RAY DIFFRACTIONr_chiral_restr0.0930.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021883
X-RAY DIFFRACTIONr_nbd_refined0.1830.2990
X-RAY DIFFRACTIONr_nbtor_refined0.30.21634
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2142
X-RAY DIFFRACTIONr_metal_ion_refined0.2220.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1480.26
X-RAY DIFFRACTIONr_mcbond_it5.7523.6871158
X-RAY DIFFRACTIONr_mcangle_it7.3186.5631444
X-RAY DIFFRACTIONr_scbond_it7.5934.2171279
X-RAY DIFFRACTIONr_scangle_it9.4227.4761859
X-RAY DIFFRACTIONr_lrange_it10.34139.9273583
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
1.891-1.940.3431330.27724020.2825960.9370.94997.65020.245
1.94-1.9930.3271310.25824000.26125310.9340.9561000.223
1.993-2.0510.2461170.22123500.22224670.9610.9681000.19
2.051-2.1140.2761170.22322900.22524070.9470.9671000.193
2.114-2.1830.2871100.22521970.22723070.9470.9661000.191
2.183-2.260.271090.22721600.22922690.9490.9661000.195
2.26-2.3450.2731000.22520550.22721550.9560.9671000.19
2.345-2.440.228960.20720160.20821120.9640.9721000.179
2.44-2.5490.2491010.21119220.21320230.9620.9721000.181
2.549-2.6730.222860.21618430.21619290.9680.9711000.188
2.673-2.8170.228990.22117390.22218380.9650.971000.194
2.817-2.9870.296890.23816630.24117520.9390.9641000.218
2.987-3.1920.259740.2215760.22216500.960.9691000.207
3.192-3.4470.221950.2114530.21115480.9720.9731000.201
3.447-3.7740.217690.1913490.19114180.9710.981000.185
3.774-4.2160.215760.15812260.16113030.9730.98699.92330.162
4.216-4.8630.131390.13111230.13111620.9930.9911000.138
4.863-5.940.183500.1649420.1659920.9790.9841000.171
5.94-8.3390.232390.2167580.2167970.9660.9781000.223
8.339-48.520.156280.2174680.2144980.9740.97299.59840.23

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