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- PDB-9n53: Glutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-AAATTT DNA conju... -

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Basic information

Entry
Database: PDB / ID: 9n53
TitleGlutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-AAATTT DNA conjugate in P 4 21 2 space group
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
: / 1-ETHYL-PYRROLIDINE-2,5-DIONE / Glutarate 2-hydroxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 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 3, 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
B: Glutarate 2-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8115
Polymers74,5722
Non-polymers2393
Water8,395466
1
A: Glutarate 2-hydroxylase
B: Glutarate 2-hydroxylase
hetero molecules

A: Glutarate 2-hydroxylase
B: Glutarate 2-hydroxylase
hetero molecules

A: Glutarate 2-hydroxylase
B: Glutarate 2-hydroxylase
hetero molecules

A: Glutarate 2-hydroxylase
B: Glutarate 2-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,24520
Polymers298,2908
Non-polymers95512
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Unit cell
Length a, b, c (Å)123.840, 123.840, 127.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-652-

HOH

21A-691-

HOH

31A-742-

HOH

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Components

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


Mass: 37286.203 Da / Num. of mol.: 2 / Mutation: K270C
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-NEN / 1-ETHYL-PYRROLIDINE-2,5-DIONE


Mass: 127.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
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: 3.27 Å3/Da / Density % sol: 62.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.08 M Sodium chloride, 0.04 M Sodium cacodylate trihydrate pH 7.0, 30 % v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 1.65→34.62 Å / Num. obs: 118646 / % possible obs: 100 % / Redundancy: 16.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.047 / Rrim(I) all: 0.14 / Χ2: 1.02 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.04-34.6214.30.0256684210.0090.0270.5998.3
1.65-1.6816.53.4140.958110.3561.2393.6341.03100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDS20230630data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→34.62 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21535 5800 4.9 %RANDOM
Rwork0.19169 ---
obs0.19285 112806 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.777 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1.34 Å2
Refinement stepCycle: 1 / Resolution: 1.65→34.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 9 466 5063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0124727
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.521.8316388
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0175559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.559537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88910795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023648
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_it7.4971.6662251
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.4262.9852805
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it12.8082.1662476
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined20.7320.357124
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.38134727
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 379 -
Rwork0.328 8283 -
obs--99.99 %

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