PDB-7hka: Crystal Structure of N-methylhydantoinase in complex with 1-methy...

ID or keywords:

Entry

Database: PDB / ID: 7hka

Title

Crystal Structure of N-methylhydantoinase in complex with 1-methylimidazolidine-2,4-dione, C-terminal residues visible

Components

N-methylhydantoinase

Keywords

HYDROLASE / ATPASE / NMH / DHU / ATP-BINDING / CREATINE METABOLISM

Function / homology

: / AMMONIUM ION

Function and homology information

Biological species

Glutamicibacter protophormiae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.07 Å

Authors

Stihle, M. / Benz, J. / Asztalos, P. / Rudolph, M.G.

Funding support

Switzerland, 1items

Citation

Journal: To be published
Title: Crystal Structure of a N-methylhydantoinase complex
Authors: Asztalos, P. / Meier, T. / Clairfeuille, T. / Rudolph, M.G.

History

Deposition	Oct 10, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 15, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7hka.cif.gz	994.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7hka.ent.gz		Display	PDB format
PDBx/mmJSON format	7hka.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hk/7hka ftp://data.pdbj.org/pub/pdb/validation_reports/hk/7hka	HTTPS FTP

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Group deposition

ID	G_1002306 (6 entries) 7hk5 7hk6 7hk7 7hk8 7hk9 7hka
Title	To be published
Type	undefined
Description	A set of nmhase crystal structures

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#135 - Mar 2011 Integrase similarity (1)

Deposited unit

A: N-methylhydantoinase

B: N-methylhydantoinase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, elutes as a dimer

Unit cell

Length a, b, c (Å)	216.645, 216.645, 132.692
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	94
Space group name H-M	P4₂2₁2

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Protein , 1 types, 2 molecules AB

#1: Protein	N-methylhydantoinase Mass: 140124.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glutamicibacter protophormiae (bacteria) Plasmid: pBP010 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101

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Non-polymers , 6 types, 1320 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-A1BC1 / 1-methylimidazolidine-2,4-dione Mass: 114.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#5: Chemical	ChemComp-NH4 / AMMONIUM ION Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₄N
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1300 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.78 Å³/Da / Density % sol: 55.72 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 8-21 mg/ml protein in 20mM HEPES/NaOH pH 7.4, 0.1 M NaCl, 100 mM MgCl2, 30mM NH4Cl mixed 1+1 with 0.2 M ammonium acetate, 0.1 M Bis-Tris/HCl pH 5.5, 25.000 %w/v PEG 3350, 3 %v/v TMAO

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1.00001 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2018

Radiation

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

Radiation wavelength

Wavelength: 1.00001 Å / Relative weight: 1

Reflection

Resolution: 2.07→96.89 Å / Num. obs: 190426 / % possible obs: 99.9 % / Redundancy: 13.524 % / B_iso Wilson estimate: 34.12 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.219 / R_rim(I) all: 0.227 / Χ²: 0.757 / Net I/σ(I): 11.49 / Num. measured all: 2575235 / Scaling rejects: 315

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.07-2.12	13.951	3.814	0.76	194314	13937	13928	0.322	3.958	99.9
2.12-2.18	13.871	3.053	0.99	188851	13627	13615	0.417	3.17	99.9
2.18-2.25	13.731	2.359	1.28	181382	13218	13210	0.523	2.45	99.9
2.25-2.31	13.368	1.862	1.63	171290	12822	12813	0.654	1.935	99.9
2.31-2.39	12.859	1.509	1.99	160069	12456	12448	0.725	1.571	99.9
2.39-2.47	14.092	1.208	2.57	170287	12088	12084	0.818	1.253	100
2.47-2.57	13.995	1.001	3.12	163248	11674	11665	0.858	1.038	99.9
2.57-2.67	13.797	0.798	3.84	154734	11221	11215	0.908	0.829	99.9
2.67-2.79	13.435	0.613	4.91	145278	10818	10813	0.938	0.638	100
2.79-2.93	12.754	0.441	6.57	131273	10295	10293	0.964	0.459	100
2.93-3.09	14.061	0.338	8.88	138642	9863	9860	0.981	0.351	100
3.09-3.27	13.879	0.236	12.46	128871	9287	9285	0.99	0.245	100
3.27-3.5	13.673	0.16	17.6	120231	8796	8793	0.995	0.166	100
3.5-3.78	12.737	0.11	23.82	104278	8189	8187	0.997	0.115	100
3.78-4.14	13.661	0.082	31.23	103236	7559	7557	0.999	0.085	100
4.14-4.63	13.606	0.062	39.48	93515	6873	6873	0.999	0.065	100
4.63-5.34	12.833	0.057	40.56	78266	6101	6099	0.999	0.06	100
5.34-6.55	12.888	0.063	37.49	67171	5212	5212	0.999	0.066	100
6.55-9.26	12.896	0.04	51.68	52615	4082	4080	1	0.042	100
9.26-83.91	11.554	0.027	65.34	27684	2409	2396	1	0.028	99.5

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.21.1_5286	refinement
PDB_EXTRACT	3.28	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.07→83.91 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.5 / Stereochemistry target values: ML / Details: some additional residues visible at the C-terminus

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2027	7644	5.05 %	RANDOM
R_work	0.163	143778	-	-
obs	0.165	151422	80 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 165.15 Å² / B_iso mean: 42.917 Å² / B_iso min: 17.35 Å²

Refinement step

Cycle: final / Resolution: 2.07→83.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19605	0	108	1300	21013
B_iso mean	-	-	69.01	41.75	-
Num. residues	-	-	-	-	2561

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.07-2.1	0.2069	23	0.2336	521	544	9
2.1-2.12	0.3054	49	0.2392	1112	1161	19
2.12-2.15	0.2722	80	0.2418	1773	1853	30
2.15-2.18	0.2953	131	0.2388	2210	2341	38
2.18-2.2	0.2855	137	0.2359	2648	2785	45
2.2-2.23	0.2753	192	0.2324	3027	3219	52
2.23-2.27	0.2533	178	0.2252	3379	3557	57
2.27-2.3	0.2548	214	0.2207	3551	3765	60
2.3-2.34	0.2549	212	0.2218	3823	4035	64
2.34-2.37	0.2657	230	0.2155	4167	4397	70
2.37-2.42	0.2577	237	0.2172	4459	4696	75
2.42-2.46	0.2641	275	0.2152	4935	5210	83
2.46-2.51	0.2711	288	0.2258	5607	5895	95
2.51-2.56	0.2669	302	0.2208	5967	6269	99
2.56-2.61	0.2646	335	0.2088	5917	6252	100
2.61-2.67	0.2612	346	0.1993	5963	6309	100
2.67-2.74	0.2464	355	0.197	5908	6263	100
2.74-2.82	0.2367	291	0.1948	5986	6277	100
2.82-2.9	0.2165	295	0.1884	5955	6250	100
2.9-2.99	0.2393	311	0.1883	6010	6321	100
2.99-3.1	0.2217	332	0.1876	5989	6321	100
3.1-3.22	0.2151	309	0.1832	5991	6300	100
3.22-3.37	0.2243	329	0.1748	6001	6330	100
3.37-3.55	0.2078	314	0.1517	5999	6313	100
3.55-3.77	0.1836	288	0.1371	6050	6338	100
3.77-4.06	0.1862	329	0.1302	6049	6378	100
4.06-4.47	0.1478	311	0.1133	6063	6374	100
4.47-5.11	0.1378	305	0.1121	6132	6437	100
5.12-6.44	0.1679	283	0.1433	6206	6489	100
6.44-83.91	0.163	363	0.1471	6380	6743	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.4806	0.0746	0.0601	0.6102	0.188	0.4711	0.0161	0.0602	-0.0449	-0.0411	-0.0587	-0.1906	0.1432	0.0391	-0.0001	0.3349	0.034	0.0841	0.2362	0.0107	0.2603	50.9513	-6.9733	19.3829
2	0.363	0.15	-0.1322	0.3186	-0.3396	0.2807	-0.0273	0.1476	-0.116	-0.1437	0.0022	-0.0466	0.0947	-0.0001	-0	0.3601	-0.0111	0.0539	0.2737	-0.0322	0.2853	39.6029	-13.1963	18.673
3	0.1761	0.2607	0.1934	0.4514	0.422	0.3086	-0.0263	0.0214	-0.0731	0.2216	0.0099	-0.1583	0.1715	0.1222	0	0.4581	0.0228	0.0085	0.3546	0.0489	0.4398	26.7026	-22.1893	45.9697
4	0.7203	-0.1375	-0.1375	0.4552	-0.042	0.1782	-0.0165	0.1665	-0.0403	-0.2347	-0.0336	0.112	0.0562	-0.0867	0	0.4338	-0.022	-0.0046	0.3299	-0.0268	0.2649	27.7297	-3.6203	12.2389
5	0.2729	0.1357	-0.2013	0.6446	0.0369	0.1566	-0.1121	0.0015	-0.1361	-0.0275	0.0222	0.1527	0.0342	-0.016	-0	0.3116	-0.0196	0.0289	0.2649	-0.0061	0.4196	17.1927	-25.0694	31.6688
6	0.2625	-0.1189	0.0281	0.5804	-0.0123	0.1368	-0.0274	-0.0233	0.0144	0.0285	-0.0071	0.0027	0.0174	-0.0116	-0	0.2335	-0.0027	-0.005	0.2062	0.0091	0.1928	32.0092	17.1228	42.4548
7	0.3817	0.0518	-0.2548	-0.0604	0.1713	0.4618	-0.0404	-0.0868	0.0803	-0.0318	0.0834	-0.1867	0.0077	0.1822	-0.0009	0.2398	-0.0047	-0.0055	0.2988	0.0009	0.3419	64.4157	13.555	41.8833
8	0.8539	-0.0676	0.1085	0.5867	0.0976	0.3778	-0.0472	-0.098	0.2354	0.0543	0.0322	0.0572	-0.195	-0.0976	-0	0.3843	0.0559	-0.0366	0.2604	-0.038	0.3353	3.3822	82.3803	48.9489
9	0.5629	-0.2747	0.2605	0.5358	-0.0694	0.361	-0.0239	-0.0398	0.0627	0.0051	0.015	0.1655	-0.0904	-0.0696	0	0.2887	0.0442	-0.0449	0.2849	0.0168	0.3135	-8.5054	70.6135	38.1299
10	0.3087	-0.1509	-0.1195	0.3461	-0.0054	0.1613	-0.0648	0.0755	0.0444	-0.0219	0.0149	0.2712	-0.0535	-0.1457	-0.0006	0.3103	0.0844	-0.1074	0.3607	0.0118	0.5049	-23.4845	74.3916	26.8023
11	0.298	-0.0386	-0.1198	0.4169	-0.0451	0.184	0.0161	0.0302	0.055	-0.0795	-0.0136	-0.0574	-0.0401	0.0203	-0	0.2846	-0.0096	-0.0155	0.2111	0.0217	0.2271	21.631	59.9927	27.7386

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 202 )	A	1 - 202
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 203 through 327 )	A	203 - 327
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 328 through 438 )	A	328 - 438
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 439 through 603 )	A	439 - 603
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 604 through 726 )	A	604 - 726
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 727 through 1186 )	A	727 - 1186
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1187 through 1288 )	A	0
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 328 )	B	1 - 328
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 329 through 603 )	B	329 - 603
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 604 through 726 )	B	604 - 726
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 727 through 1283 )	B	727 - 1283

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