PDB-9n5s: Glutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-GC DNA conjugate

ID or keywords:

Entry

Database: PDB / ID: 9n5s

Title

Glutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-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: 2.73 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	Feb 4, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2026	Provider: repository / Type: Initial release
Revision 1.1	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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Download

PDBx/mmCIF format	9n5s.cif.gz	75.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9n5s.ent.gz	54.5 KB	Display	PDB format
PDBx/mmJSON format	9n5s.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n5/9n5s ftp://data.pdbj.org/pub/pdb/validation_reports/n5/9n5s	HTTPS FTP

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Related structure data

Related structure data	9n2uC 9n33C 9n34C 9n53C 9n56C 9n57C 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

hetero molecules

37.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glutarate 2-hydroxylase

hetero molecules

x 8

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

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-x,-y,z	1
crystal symmetry operation	3_555	-y,x,z	1
crystal symmetry operation	4_555	y,-x,z	1
crystal symmetry operation	5_555	-x,y,-z	1
crystal symmetry operation	6_555	x,-y,-z	1
crystal symmetry operation	7_555	y,x,-z	1
crystal symmetry operation	8_555	-y,-x,-z	1

Unit cell

Length a, b, c (Å)	122.525, 122.525, 136.661
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	97
Space group name H-M	I422

#1: Protein	Glutarate 2-hydroxylase / G-2-H Mass: 37286.203 Da / Num. of mol.: 1 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.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.44 Å³/Da / Density % sol: 64.23 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 20 % v/v Glycerol, 5 % w/v PEG 3350, 0.05 M Bis-Tris pH 7, 1 M Ammonium sulfate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.976284 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 8, 2023

Radiation

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

Radiation wavelength

Wavelength: 0.976284 Å / Relative weight: 1

Reflection

Resolution: 2.73→53.65 Å / Num. obs: 14176 / % possible obs: 100 % / Redundancy: 26.7 % / CC_1/2: 0.995 / R_merge(I) obs: 0.381 / R_pim(I) all: 0.105 / R_rim(I) all: 0.395 / Χ²: 0.97 / Net I/σ(I): 7.4

Reflection shell

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	% possible all
9.05-53.65	23.6	0.087	18.1	452	0.998	0.024	0.09	0.4	99.7
2.73-2.86	27.6	2.667	1.7	1846	0.865	0.726	2.764	0.97	100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
Coot	0.9.8.92	model building
DIALS	3.17.0	data reduction
Aimless	0.7.15	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.73→50.911 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.93 / Cross valid method: FREE R-VALUE / ESU R: 0.41 / ESU R Free: 0.258 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2197	674	4.764 %
R_work	0.1865	13473	-
all	0.188	-	-
obs	-	14147	99.767 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 58.77 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.04 Å²	-0 Å²	0 Å²
2-	-	3.04 Å²	-0 Å²
3-	-	-	-6.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.73→50.911 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2357	0	11	40	2408

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	2426
X-RAY DIFFRACTION	r_angle_refined_deg	1.861	1.831	3285
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.615	5	286
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	20.006	5	20
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.443	10	407
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.506	10	127
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	355
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1875
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	997
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	1618
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.167	0.2	74
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.227	0.2	37
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.081	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	6.032	5.679	1153
X-RAY DIFFRACTION	r_mcangle_it	8.888	10.162	1436
X-RAY DIFFRACTION	r_scbond_it	7.134	5.998	1273
X-RAY DIFFRACTION	r_scangle_it	9.918	10.82	1849
X-RAY DIFFRACTION	r_lrange_it	12.189	59.345	3490

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
2.73-2.801	0.339	38	0.301	979	0.302	1023	0.907	0.927	99.4135	0.288
2.801-2.877	0.308	48	0.273	938	0.275	992	0.924	0.943	99.3952	0.257
2.877-2.96	0.299	35	0.268	949	0.269	988	0.932	0.948	99.5951	0.25
2.96-3.051	0.288	48	0.269	897	0.27	946	0.938	0.951	99.8943	0.247
3.051-3.151	0.277	42	0.231	870	0.233	914	0.951	0.963	99.7812	0.209
3.151-3.261	0.248	54	0.211	836	0.214	891	0.959	0.969	99.8878	0.187
3.261-3.384	0.27	44	0.198	800	0.201	846	0.948	0.974	99.7636	0.176
3.384-3.521	0.237	34	0.179	804	0.181	839	0.97	0.98	99.8808	0.155
3.521-3.677	0.184	44	0.178	760	0.178	806	0.972	0.981	99.7519	0.158
3.677-3.855	0.186	40	0.168	715	0.17	755	0.975	0.981	100	0.151
3.855-4.063	0.176	37	0.159	696	0.16	733	0.981	0.984	100	0.147
4.063-4.307	0.256	40	0.156	644	0.161	684	0.964	0.985	100	0.145
4.307-4.602	0.17	32	0.142	633	0.143	665	0.981	0.988	100	0.138
4.602-4.968	0.184	28	0.143	581	0.144	609	0.982	0.988	100	0.134
4.968-5.437	0.152	27	0.152	540	0.152	567	0.99	0.988	100	0.147
5.437-6.07	0.165	21	0.192	492	0.191	516	0.984	0.982	99.4186	0.183
6.07-6.992	0.288	19	0.213	445	0.216	464	0.979	0.977	100	0.203
6.992-8.524	0.114	17	0.171	390	0.168	407	0.994	0.984	100	0.174
8.524-11.889	0.115	8	0.137	310	0.137	318	0.995	0.989	100	0.143
11.889-50.911	0.392	18	0.249	194	0.258	212	0.884	0.956	100	0.253

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