PDB-9n2u: Glutarate L-2-hydroxylase N187C mutant-5'-Mal-C6-GC DNA conjugate

ID or keywords:

Entry

Database: PDB / ID: 9n2u

Title

Glutarate L-2-hydroxylase N187C mutant-5'-Mal-C6-GC 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: 2.06 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
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	9n2u.cif.gz	222.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9n2u.ent.gz		Display	PDB format
PDBx/mmJSON format	9n2u.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n2/9n2u ftp://data.pdbj.org/pub/pdb/validation_reports/n2/9n2u	HTTPS FTP

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Related structure data

Related structure data	9n33C 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

75.2 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
301 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	124.083, 124.083, 126.932
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.: 2 / 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.: 146 / 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: 3.27 Å³/Da / Density % sol: 62.44 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.05 M Bis-Tris pH 7, 1.5 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 23, 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: 2.06→126.93 Å / Num. obs: 61788 / % possible obs: 100 % / Redundancy: 28.5 % / CC_1/2: 0.997 / R_merge(I) obs: 0.361 / R_pim(I) all: 0.096 / R_rim(I) all: 0.373 / Χ²: 0.97 / Net I/σ(I): 8

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
9.21-126.93	23.9	0.079	25.5	827	0.999	0.021	0.082	0.63
2.06-2.11	29.7	2.992	1.6	4522	0.601	0.789	3.095	0.96

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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: 2.06→126.93 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.944 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.134
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2228	3182	5.156 %
R_work	0.2003	58534	-
all	0.201	-	-
obs	-	61716	99.934 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 35.675 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.36 Å²	0 Å²	0 Å²
2-	-	-0.36 Å²	0 Å²
3-	-	-	0.721 Å²

Refinement step

Cycle: LAST / Resolution: 2.06→126.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4601	0	26	146	4773

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	4758
X-RAY DIFFRACTION	r_bond_other_d	0	0.016	4480
X-RAY DIFFRACTION	r_angle_refined_deg	1.573	1.833	6442
X-RAY DIFFRACTION	r_angle_other_deg	0.513	1.765	10279
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.246	5	562
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	18.972	5	37
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.51	5	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.475	10	806
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.508	10	245
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	696
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5643
X-RAY DIFFRACTION	r_gen_planes_other	0.01	0.02	1161
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	780
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.209	0.2	3884
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	2233
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	2479
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	165
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.114	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.221	0.2	89
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.151	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	2.964	3.199	2260
X-RAY DIFFRACTION	r_mcbond_other	2.964	3.199	2260
X-RAY DIFFRACTION	r_mcangle_it	4.21	5.714	2818
X-RAY DIFFRACTION	r_mcangle_other	4.211	5.715	2819
X-RAY DIFFRACTION	r_scbond_it	4.315	3.809	2498
X-RAY DIFFRACTION	r_scbond_other	4.298	3.806	2496
X-RAY DIFFRACTION	r_scangle_it	6.52	6.749	3624
X-RAY DIFFRACTION	r_scangle_other	6.519	6.75	3625
X-RAY DIFFRACTION	r_lrange_it	8.091	31.279	5024
X-RAY DIFFRACTION	r_lrange_other	8.089	31.229	5006
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.06	0.05	9489

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	0.06049	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.06049	0.0501

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
2.06-2.114	0.265	218	0.275	4295	0.274	4520	0.949	0.948	99.8451	0.27
2.114-2.171	0.287	246	0.257	4113	0.259	4362	0.943	0.956	99.9312	0.247
2.171-2.234	0.277	235	0.243	4027	0.244	4268	0.955	0.962	99.8594	0.23
2.234-2.303	0.264	190	0.24	3985	0.241	4176	0.956	0.963	99.9761	0.226
2.303-2.379	0.25	182	0.22	3816	0.221	4000	0.964	0.97	99.95	0.203
2.379-2.462	0.266	177	0.228	3713	0.229	3892	0.954	0.97	99.9486	0.208
2.462-2.555	0.264	207	0.219	3549	0.222	3761	0.962	0.973	99.8671	0.197
2.555-2.659	0.246	185	0.21	3437	0.212	3628	0.966	0.974	99.8346	0.189
2.659-2.777	0.253	209	0.209	3284	0.212	3494	0.955	0.973	99.9714	0.188
2.777-2.913	0.256	168	0.218	3171	0.22	3340	0.957	0.969	99.9701	0.198
2.913-3.07	0.25	159	0.22	3015	0.222	3174	0.959	0.97	100	0.199
3.07-3.257	0.243	150	0.206	2880	0.208	3031	0.963	0.974	99.967	0.191
3.257-3.481	0.206	157	0.185	2698	0.186	2856	0.977	0.981	99.965	0.171
3.481-3.76	0.177	111	0.169	2552	0.17	2664	0.984	0.984	99.9625	0.157
3.76-4.118	0.167	142	0.149	2312	0.15	2454	0.984	0.987	100	0.138
4.118-4.604	0.166	139	0.14	2108	0.142	2248	0.985	0.988	99.9555	0.13
4.604-5.315	0.201	105	0.177	1888	0.178	1993	0.976	0.983	100	0.162
5.315-6.507	0.25	91	0.222	1621	0.224	1713	0.967	0.973	99.9416	0.206
6.507-9.19	0.206	78	0.22	1280	0.219	1358	0.975	0.971	100	0.205
9.19-126.93	0.215	33	0.221	790	0.221	825	0.968	0.97	99.7576	0.255

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