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- PDB-9n56: Glutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-AGCT DNA conjugate -

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Basic information

Entry
Database: PDB / ID: 9n56
TitleGlutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-AGCT DNA conjugate
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: 2.25 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)75,0688
Polymers74,5722
Non-polymers4966
Water4,143230
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)300,27332
Polymers298,2908
Non-polymers1,98424
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)124.414, 124.414, 128.175
Angle α, β, γ (deg.)90, 90, 90
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-527-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 18 - 316 / Label seq-ID: 18 - 316

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 37286.203 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 230 / 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: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.3 M Lithium sulfate, 0.05 M Bis-Tris pH 7, 18 % w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976284 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976284 Å / Relative weight: 1
ReflectionResolution: 2.25→64.09 Å / Num. obs: 48353 / % possible obs: 100 % / Redundancy: 26.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.043 / Rrim(I) all: 0.163 / Χ2: 0.84 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9-64.0924.40.038608830.9990.010.0390.5899.8
2.25-2.3226.51.7472.243790.8930.4931.8151.16100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DIALS3.17.0data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→51.091 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: FREE R-VALUE / ESU R: 0.213 / ESU R Free: 0.175 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 2347 4.884 %RANDOM
Rwork0.2136 45707 --
all0.215 ---
obs-48054 99.431 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.662 Å2
Baniso -1Baniso -2Baniso -3
1--1.071 Å20 Å20 Å2
2---1.071 Å20 Å2
3---2.141 Å2
Refinement stepCycle: LAST / Resolution: 2.25→51.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4660 0 22 230 4912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124804
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.8316516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.636538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11910805
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.31210248
X-RAY DIFFRACTIONr_chiral_restr0.0580.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023714
X-RAY DIFFRACTIONr_nbd_refined0.1920.21904
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23224
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2262
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1770.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.223
X-RAY DIFFRACTIONr_mcbond_it1.9244.6472287
X-RAY DIFFRACTIONr_mcangle_it3.1188.3332850
X-RAY DIFFRACTIONr_scbond_it2.2325.0062517
X-RAY DIFFRACTIONr_scangle_it3.7639.0953666
X-RAY DIFFRACTIONr_lrange_it5.7350.1176974
X-RAY DIFFRACTIONr_ncsr_local_group_10.0610.059529
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.060860.0501
12BX-RAY DIFFRACTIONLocal ncs0.060860.0501
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
2.25-2.3080.5491400.55231800.55234940.6360.62995.020.587
2.308-2.3710.2681640.27632660.27534450.9510.94899.56460.26
2.371-2.440.2641510.26231590.26233230.950.95699.60880.237
2.44-2.5150.2921410.26730810.26832320.9450.95299.69060.24
2.515-2.5970.2641650.24729680.24831380.9580.96399.84070.218
2.597-2.6880.2661360.26828900.26830390.9520.95499.57220.237
2.688-2.7890.291180.2528210.25229450.9490.96399.79630.212
2.789-2.9030.2351220.23727090.23728360.9610.96699.82370.203
2.903-3.0310.2671660.24525720.24627380.9560.9641000.211
3.031-3.1790.271370.22724540.22925930.9560.96799.92290.198
3.179-3.350.2321100.20823800.20924920.9660.97299.91970.183
3.35-3.5520.2371360.21422250.21623660.9650.97199.78870.19
3.552-3.7960.222970.19921330.222340.970.97699.82090.176
3.796-4.0990.1981450.16919280.17120830.980.98399.51990.151
4.099-4.4870.1851210.14218130.14519340.9820.9881000.132
4.487-5.0120.167720.14416830.14517550.9860.9881000.136
5.012-5.7780.178750.17415010.17415760.9820.9841000.164
5.778-7.0540.213550.20612890.20613440.9740.9751000.193
7.054-9.8820.214420.17310430.17410850.9730.9811000.168
9.882-51.0910.208540.236120.2286670.9790.96399.85010.227

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