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- PDB-9n7j: Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-TTTT DNA conjuga... -

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Basic information

Entry
Database: PDB / ID: 9n7j
TitleGlutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-TTTT DNA conjugate at 3.12 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: 3.121 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 5, 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)74,6864
Polymers74,5752
Non-polymers1122
Water362
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)298,74516
Polymers298,2988
Non-polymers4478
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Unit cell
Length a, b, c (Å)124.759, 124.759, 137.221
Angle α, β, γ (deg.)90, 90, 90
Int Tables number90
Space group name H-MP4212
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: ALA / End label comp-ID: ALA / Auth seq-ID: 18 - 315 / Label seq-ID: 18 - 315

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: 37287.254 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.58 Å3/Da / Density % sol: 65.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES monohydrate pH 6.5, 1.6 M Magnesium sulfate heptahydrate

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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: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 3.12→92.31 Å / Num. obs: 19914 / % possible obs: 100 % / Redundancy: 14.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.378 / Rpim(I) all: 0.142 / Rrim(I) all: 0.404 / Χ2: 1.02 / Net I/σ(I): 6.9
Reflection shell

% possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
8.83-92.3113.30.09221.510040.9980.0330.0980.94
3.12-3.3414.72.1751.435290.5410.8392.3321.02

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
Coot0.9.8.92model building
XDS20220820data reduction
Aimless0.7.15data scaling
PHASER5.8.0430phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.121→88.374 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.905 / Cross valid method: FREE R-VALUE / ESU R: 2.086 / ESU R Free: 0.364 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2325 1001 5.038 %
Rwork0.2247 18869 -
all0.225 --
obs-19870 99.859 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 67.773 Å2
Baniso -1Baniso -2Baniso -3
1--3.449 Å20 Å20 Å2
2---3.449 Å20 Å2
3---6.898 Å2
Refinement stepCycle: LAST / Resolution: 3.121→88.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4576 0 2 2 4580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124698
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.8356366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7535557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.727538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01110795
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.59810244
X-RAY DIFFRACTIONr_chiral_restr0.0570.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023631
X-RAY DIFFRACTIONr_nbd_refined0.2190.22026
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23205
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2113
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.23
X-RAY DIFFRACTIONr_mcbond_it2.7746.5872240
X-RAY DIFFRACTIONr_mcangle_it4.66111.8222790
X-RAY DIFFRACTIONr_scbond_it2.916.8992458
X-RAY DIFFRACTIONr_scangle_it4.94712.5773575
X-RAY DIFFRACTIONr_lrange_it7.57670.2566884
X-RAY DIFFRACTIONr_ncsr_local_group_10.0980.059232
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.09760.0501
12BX-RAY DIFFRACTIONLocal ncs0.09760.0501
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
3.121-3.2020.382760.36313810.36414580.8530.86599.93140.351
3.202-3.290.323650.31513170.31513820.9280.9061000.295
3.29-3.3850.315690.29912980.313680.9390.91999.92690.271
3.385-3.4890.289720.26712510.26813230.9420.9391000.233
3.489-3.6030.21640.25312150.25112800.9670.94899.92190.224
3.603-3.730.201640.23111850.2312500.9720.95399.920.201
3.73-3.870.237660.21311450.21412110.9590.9681000.184
3.87-4.0280.225490.18911240.1911740.9610.97499.91480.164
4.028-4.2070.22530.1910630.19211170.9650.97599.91050.166
4.207-4.4110.184610.18510050.18510660.9790.9781000.163
4.411-4.6490.138450.1819840.17910300.9850.97999.90290.16
4.649-4.9310.218470.1819160.1839640.9720.97999.89630.16
4.931-5.270.181490.2048790.2029290.980.97499.89240.179
5.27-5.690.214380.2068190.2078580.9690.97299.88340.183
5.69-6.2310.227480.267490.2587980.9610.95999.87470.231
6.231-6.9620.289350.2676900.2687260.960.95399.86230.239
6.962-8.0310.234320.2256220.2256560.9690.96799.69510.21
8.031-9.8160.241260.1925370.1945650.9550.98199.6460.193
9.816-13.7960.162230.194270.1894520.9880.9899.55750.191
13.796-88.3740.443190.3322620.342890.7960.91697.23180.355

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