PDB-9n33: Glutarate L-2-hydroxylase N187C mutant-5'-Mal-C6-AGCT DNA conjugate

ID or keywords:

Entry

Database: PDB / ID: 9n33

Title

Glutarate L-2-hydroxylase N187C mutant-5'-Mal-C6-AGCT DNA conjugate

Components

Glutarate 2-hydroxylase

Keywords

METAL 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

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.61 Å

Authors

Han, Z. / Mirkin, C.A.

Funding support

United States, 2items

Citation

Journal: Sci Adv / Year: 2026
Title: Diffraction-quality, ultraflexible protein single crystals engineered with DNA.
Authors: Han, Z. / Mirkin, C.A.

History

Deposition	Jan 29, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 4, 2026	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2026	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Aug 12, 2026	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9n33.cif.gz	222.7 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n3/9n33 ftp://data.pdbj.org/pub/pdb/validation_reports/n3/9n33	HTTPS FTP

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Related structure data

Related structure data	9n2uC 9n34C 9n53C 9n56C 9n57C 9n5sC 9n5wC 9n60C 9n6sC 9n7cC 9n7hC 9n7iC 9n7jC 9n7lC 9n7nC 9n7pC 9n7uC 9n7xC 9n8cC 9n8dC 9n8kC 9n8lC 9n8oC 9n8sC 9n8tC 9n8uC 9n8vC 9bwu C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1)

Deposited unit

A: Glutarate 2-hydroxylase

B: Glutarate 2-hydroxylase

hetero molecules

75.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author
Evidence: gel filtration
302 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	124.937, 124.937, 127.288
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	90
Space group name H-M	P42₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 17 - 316 / Label seq-ID: 17 - 316

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

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

#1: Protein	Glutarate 2-hydroxylase / G-2-H Mass: 37301.281 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-A1BVO / (1r,4r)-4-[(2,5-dioxopyrrolidin-1-yl)methyl]cyclohexane-1-carboxamide Mass: 238.283 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₂H₁₈N₂O₃ / 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.: 14 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.33 Å³/Da / Density % sol: 63.05 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium chloride, 0.1 M Potassium chloride, 0.05 M HEPES pH 6.5, 1.9 M Lithium sulfate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID30B / Wavelength: 0.87313 Å

Detector

Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 24, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.87313 Å / Relative weight: 1

Reflection

Resolution: 2.61→127.29 Å / Num. obs: 31317 / % possible obs: 100 % / Redundancy: 28.2 % / CC_1/2: 0.997 / R_merge(I) obs: 0.373 / R_pim(I) all: 0.099 / R_rim(I) all: 0.386 / Χ²: 1.01 / Net I/σ(I): 9.2

Reflection shell

% possible all: 100

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²
9.04-127.29	24.6	0.072	30.1	879	0.999	0.019	0.074	0.84
2.61-2.73	29.6	3.455	1.6	3757	0.646	0.907	3.572	0.98

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
XDS	20230630	data reduction
Aimless	0.7.15	data scaling
PHASER	2.8.3	phasing
Coot	0.9.8.92	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.61→127.288 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.934 / Cross valid method: FREE R-VALUE / ESU R: 0.34 / ESU R Free: 0.253
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2397	1529	4.891 %
R_work	0.1956	29730	-
all	0.198	-	-
obs	-	31259	99.891 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 55.189 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.463 Å²	0 Å²	0 Å²
2-	-	-1.463 Å²	0 Å²
3-	-	-	2.926 Å²

Refinement step

Cycle: LAST / Resolution: 2.61→127.288 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4638	0	31	14	4683

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	4805
X-RAY DIFFRACTION	r_bond_other_d	0	0.016	4514
X-RAY DIFFRACTION	r_angle_refined_deg	1.739	1.833	6508
X-RAY DIFFRACTION	r_angle_other_deg	0.568	1.763	10368
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.539	5	568
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	24.625	5	37
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.446	10	807
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.092	10	244
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	701
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5689
X-RAY DIFFRACTION	r_gen_planes_other	0.01	0.02	1159
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	801
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.219	0.2	4049
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	2258
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	2610
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	72
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.219	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.234	0.2	107
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.138	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	9.031	5.03	2284
X-RAY DIFFRACTION	r_mcbond_other	9.03	5.03	2284
X-RAY DIFFRACTION	r_mcangle_it	11.032	9.02	2848
X-RAY DIFFRACTION	r_mcangle_other	11.033	9.02	2849
X-RAY DIFFRACTION	r_scbond_it	13.009	5.891	2521
X-RAY DIFFRACTION	r_scbond_other	12.771	5.881	2518
X-RAY DIFFRACTION	r_scangle_it	15.048	10.424	3660
X-RAY DIFFRACTION	r_scangle_other	15.046	10.428	3661
X-RAY DIFFRACTION	r_lrange_it	15.574	47.942	4969
X-RAY DIFFRACTION	r_lrange_other	15.561	47.928	4967
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.081	0.05	9353

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08148	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.08148	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.61-2.678	0.399	132	0.334	2134	0.338	2270	0.902	0.929	99.8238	0.329
2.678-2.751	0.39	86	0.321	2123	0.323	2212	0.913	0.936	99.8644	0.307
2.751-2.831	0.262	98	0.282	2063	0.281	2164	0.955	0.947	99.8614	0.262
2.831-2.918	0.295	82	0.281	1997	0.282	2083	0.938	0.946	99.808	0.262
2.918-3.014	0.31	136	0.277	1891	0.279	2028	0.939	0.949	99.9507	0.253
3.014-3.119	0.338	108	0.249	1869	0.254	1979	0.914	0.957	99.8989	0.226
3.119-3.237	0.282	95	0.227	1813	0.229	1909	0.942	0.967	99.9476	0.203
3.237-3.369	0.275	94	0.223	1738	0.226	1832	0.954	0.967	100	0.201
3.369-3.519	0.249	111	0.202	1644	0.204	1757	0.956	0.976	99.8862	0.183
3.519-3.69	0.299	65	0.199	1634	0.202	1702	0.953	0.976	99.8237	0.181
3.69-3.89	0.229	67	0.172	1545	0.175	1612	0.966	0.982	100	0.154
3.89-4.126	0.223	46	0.141	1470	0.143	1516	0.974	0.989	100	0.127
4.126-4.41	0.204	73	0.124	1367	0.127	1440	0.976	0.99	100	0.111
4.41-4.763	0.126	87	0.113	1272	0.114	1360	0.991	0.992	99.9265	0.1
4.763-5.217	0.195	60	0.139	1195	0.142	1255	0.975	0.989	100	0.126
5.217-5.831	0.161	31	0.167	1102	0.166	1133	0.985	0.985	100	0.149
5.831-6.731	0.288	40	0.195	981	0.199	1023	0.959	0.978	99.8045	0.177
6.731-8.238	0.238	50	0.191	826	0.194	877	0.971	0.978	99.886	0.174
8.238-11.626	0.152	42	0.163	662	0.162	704	0.985	0.985	100	0.155
11.626-127.288	0.273	26	0.321	404	0.318	437	0.964	0.91	98.3982	0.407

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