PDB-7hk7: Crystal Structure of N-methylhydantoinase in complex with Mg-ADPNP

ID or keywords:

Entry

Database: PDB / ID: 7hk7

Title

Crystal Structure of N-methylhydantoinase in complex with Mg-ADPNP

Components

N-methylhydantoinase

Keywords

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

Function / homology

PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMMONIUM ION

Function and homology information

Biological species

Glutamicibacter protophormiae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.13 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	7hk7.cif.gz	1.9 MB	Display	PDBx/mmCIF format
PDB format	pdb7hk7.ent.gz	1.6 MB	Display	PDB format
PDBx/mmJSON format	7hk7.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/7hk7 ftp://data.pdbj.org/pub/pdb/validation_reports/hk/7hk7	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) #108 - Dec 2008 Hsp90 similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#135 - Mar 2011
Integrase
similarity (1)
#108 - Dec 2008
Hsp90
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: N-methylhydantoinase

B: N-methylhydantoinase

C: N-methylhydantoinase

D: N-methylhydantoinase

hetero molecules

563 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N-methylhydantoinase

B: N-methylhydantoinase

hetero molecules

defined by author
Evidence: gel filtration, elutes as a dimer
281 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: N-methylhydantoinase

D: N-methylhydantoinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.730, 84.250, 236.250
Angle α, β, γ (deg.)	93.250, 94.820, 89.070
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	(chain A and (resid 1 through 690 or resid 693 through 1306))
2	1	chain B
3	1	(chain C and (resid 1 through 690 or resid 693 through 1306))
4	1	(chain D and (resid 1 through 690 or resid 693 through 1306))

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	PRO	PRO	(chain A and (resid 1 through 690 or resid 693 through 1306))	A	A	1 - 690	1 - 690
1	2	THR	THR	NH4	NH4	(chain A and (resid 1 through 690 or resid 693 through 1306))	A	A - G	693 - 1303	693
2	1	MET	MET	NH4	NH4	chain B	B	B - J	1 - 1303	1
3	1	MET	MET	PRO	PRO	(chain C and (resid 1 through 690 or resid 693 through 1306))	C	C	1 - 690	1 - 690
3	2	THR	THR	NH4	NH4	(chain C and (resid 1 through 690 or resid 693 through 1306))	C	C - M	693 - 1303	693
4	1	MET	MET	PRO	PRO	(chain D and (resid 1 through 690 or resid 693 through 1306))	D	D	1 - 690	1 - 690
4	2	THR	THR	NH4	NH4	(chain D and (resid 1 through 690 or resid 693 through 1306))	D	D - P	693 - 1303	693

#1: Protein	N-methylhydantoinase Mass: 140124.172 Da / Num. of mol.: 4 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
#2: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NH4 / AMMONIUM ION Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H₄N
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.5 Å³/Da / Density % sol: 50.77 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 8 mg/ml protein in 20mM HEPES/NaOH pH 7.4, 0.1 M NaCl, 100 mM MgCl2, 30mM NH4Cl mixed 1+1 with 0.1 M Bicine/NaOH pH 9.0, 20 %w/v PEG 6000, 0.2 M MgCl2, 2 mM ADPNP

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 0.99986 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 26, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.99986 Å / Relative weight: 1

Reflection

Resolution: 3.13→49.38 Å / Num. obs: 92887 / % possible obs: 97.1 % / Redundancy: 1.8 % / B_iso Wilson estimate: 54.12 Å² / CC_1/2: 0.926 / R_merge(I) obs: 0.222 / R_rim(I) all: 0.314 / Χ²: 0.859 / Net I/σ(I): 3.58 / Num. measured all: 167171 / Scaling rejects: 37

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
3.13-3.21	1.67	0.943	0.75	11569	7156	6927	0.311	1.334	96.8
3.21-3.3	1.765	0.878	0.86	11651	6834	6600	0.322	1.242	96.6
3.3-3.39	1.858	0.694	1.13	12186	6768	6557	0.422	0.981	96.9
3.39-3.5	1.857	0.535	1.45	11671	6504	6284	0.548	0.756	96.6
3.5-3.61	1.846	0.443	1.74	11180	6268	6055	0.641	0.627	96.6
3.61-3.74	1.827	0.367	2.07	10850	6131	5938	0.713	0.519	96.9
3.74-3.88	1.828	0.303	2.48	10466	5886	5725	0.786	0.428	97.3
3.88-4.04	1.774	0.239	2.96	9727	5678	5483	0.863	0.338	96.6
4.04-4.22	1.668	0.195	3.54	8894	5467	5332	0.899	0.275	97.5
4.22-4.43	1.789	0.158	4.41	9156	5239	5119	0.929	0.223	97.7
4.43-4.67	1.883	0.139	5.19	9022	4914	4792	0.942	0.196	97.5
4.67-4.95	1.855	0.135	5.22	8409	4656	4532	0.948	0.19	97.3
4.95-5.29	1.847	0.144	4.85	7902	4390	4279	0.941	0.204	97.5
5.29-5.71	1.814	0.156	4.52	7191	4080	3964	0.929	0.22	97.2
5.71-6.26	1.647	0.164	3.99	6030	3752	3661	0.925	0.233	97.6
6.26-7	1.808	0.138	4.95	6097	3447	3372	0.945	0.196	97.8
7-8.08	1.89	0.092	7.32	5421	2962	2869	0.976	0.13	96.9
8.08-9.9	1.824	0.054	11.3	4509	2546	2472	0.991	0.076	97.1
9.9-14	1.691	0.043	13.52	3261	1972	1929	0.993	0.06	97.8
14-49.38	1.985	0.038	16.48	1979	1053	997	0.995	0.054	94.7

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.21.2_5419	refinement
PDB_EXTRACT	3.28	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 3.13→49.38 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.27 / Stereochemistry target values: ML
Details: large conformational changes upon ADPNP binding; not all chains have density for an NH4+ ion near residue 959;

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2645	4477	4.83 %	RANDOM
R_work	0.223	88273	-	-
obs	0.2249	92750	96.95 %	-

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 207.86 Å² / B_iso mean: 55.2702 Å² / B_iso min: 22.07 Å²

Refinement step

Cycle: final / Resolution: 3.13→49.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	39140	0	132	16	39288
B_iso mean	-	-	53.12	54.01	-
Num. residues	-	-	-	-	5118

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	24356	X-RAY DIFFRACTION	5.357	TORSIONAL
1	2	B	24356	X-RAY DIFFRACTION	5.357	TORSIONAL
1	3	C	24356	X-RAY DIFFRACTION	5.357	TORSIONAL
1	4	D	24356	X-RAY DIFFRACTION	5.357	TORSIONAL

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 (%)
3.13-3.17	0.3747	155	0.359	2915	3070	96
3.17-3.2	0.3899	150	0.3485	2991	3141	96
3.2-3.24	0.3617	159	0.3509	2873	3032	96
3.24-3.28	0.423	138	0.3539	2865	3003	96
3.28-3.33	0.3764	145	0.3435	2977	3122	97
3.33-3.37	0.3899	131	0.327	3030	3161	97
3.37-3.42	0.3583	148	0.3202	2832	2980	97
3.42-3.47	0.3583	145	0.3057	2916	3061	96
3.47-3.53	0.3278	162	0.2862	2980	3142	97
3.53-3.58	0.3197	163	0.2806	2872	3035	96
3.58-3.64	0.3136	149	0.2731	2942	3091	97
3.64-3.71	0.3051	175	0.2709	2939	3114	97
3.71-3.78	0.3124	146	0.2661	2924	3070	97
3.78-3.86	0.3163	157	0.2597	2929	3086	97
3.86-3.94	0.3134	157	0.2471	2963	3120	97
3.94-4.03	0.2797	144	0.2281	2909	3053	97
4.03-4.14	0.2377	175	0.2134	2945	3120	97
4.14-4.25	0.2652	158	0.1976	2951	3109	98
4.25-4.37	0.2218	144	0.1857	2963	3107	98
4.37-4.51	0.2354	122	0.1759	2961	3083	97
4.51-4.67	0.2016	122	0.1634	3022	3144	98
4.67-4.86	0.1918	111	0.1695	2952	3063	97
4.86-5.08	0.2088	130	0.1719	3003	3133	97
5.08-5.35	0.2285	158	0.1788	2950	3108	97
5.35-5.69	0.223	152	0.1863	2938	3090	97
5.69-6.12	0.2242	161	0.2043	2960	3121	98
6.12-6.74	0.2257	162	0.1945	2938	3100	98
6.74-7.71	0.231	125	0.166	3000	3125	97
7.71-9.7	0.1708	153	0.1353	2925	3078	97
9.7-49.38	0.1685	180	0.1527	2908	3088	97

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	0.1634	0.0463	-0.0224	0.1874	-0.1068	0.1922	0.0964	0.015	-0.0908	0.1153	-0.0962	-0.048	-0.0008	0.0842	0.0661	0.217	0.0215	-0.0948	0.1106	-0.0093	0.208	-11.7819	19.4621	49.4948
2	0.2618	0.0127	0.1302	0.4038	-0.2319	0.5178	-0.0426	-0.0017	-0.0674	0.0239	-0.0306	-0.0898	0.0405	-0.0278	-0.2814	0.1875	0.0391	-0.0284	0.0962	-0.025	0.2096	-27.3373	8.1143	38.4458
3	0.2672	-0.0473	0.0755	0.0462	0.0645	0.2366	-0.0111	0.1122	-0.005	0.0108	0.0946	0.1073	-0.0124	-0.0673	0.06	0.2133	-0.0123	-0.0032	0.1262	0.0192	0.1938	-27.4446	44.3789	27.7688
4	0.0862	-0.0533	0.2771	0.2517	-0.13	0.4234	-0.0099	0.3979	0.2746	-0.0397	0.307	0.2595	-0.2493	0.0507	0.2964	0.2195	-0.0727	-0.0274	0.2902	0.1716	0.2054	-15.7155	88.6425	-32.771
5	0.3813	-0.3094	0.1232	0.413	0.1989	0.5867	-0.051	0.8006	0.4095	0.1995	-0.1854	-0.3165	0.1244	-0.195	-0.5478	0.1529	-0.1166	-0.2228	0.655	0.2091	0.2771	6.238	81.8822	-40.8546
6	0.1398	-0.1914	0.2408	0.4695	-0.2199	0.3339	-0.0383	0.4411	0.2684	0.1152	0.0006	0.4295	0.1074	-0.0493	-0.2678	0.0758	-0.0369	-0.1721	0.4416	0.2078	0.1862	-19.653	70.4254	-39.7747
7	0.7476	-0.0315	-0.1073	0.18	-0.2511	0.2254	0.0299	0.0707	-0.0371	0.084	-0.0186	-0.0194	-0.0636	0.0624	0.1075	0.151	-0.0528	0.0055	0.1916	-0.0339	0.1247	-0.3465	69.6494	-9.3058
8	0.1923	-0.0125	-0.214	0.2944	-0.0725	0.1198	-0.0002	-0.0994	0.0142	-0.2715	-0.0249	0.0019	0.0256	-0.1195	-0.2962	0.3126	0.0174	-0.0755	0.1922	-0.0492	0.1874	-10.2313	47.3563	83.7003
9	0.1404	0.0387	0.1231	0.9665	0.4531	0.5108	-0.0658	-0.0603	-0.083	-0.0031	-0.0622	-0.0751	0.0492	-0.0372	-0.1883	0.2237	0.0028	-0.0057	0.1728	-0.0289	0.266	4.4766	37.4919	96.7558
10	0.165	-0.1144	0.0702	0.0949	0.197	0.3413	0.0496	-0.0367	-0.0364	-0.0184	0.0123	-0.0662	-0.0707	0.0771	0.3222	0.1676	0.0245	-0.007	0.2012	-0.0449	0.1719	5.6516	73.0619	105.2514
11	0.0647	-0.06	-0.055	0.0832	0.0337	0.1177	0.0019	-0.1364	0.0915	0.0182	0.1602	-0.1598	-0.1838	0.1479	0.0972	0.3399	0.0821	-0.052	0.3878	-0.0769	0.0876	-9.7934	117.3903	177.808
12	0.0286	-0.0136	0.0346	0.097	0.0023	0.1582	0.0179	-0.0958	0.0877	-0.0439	0.0523	-0.0418	-0.1311	-0.019	0.0482	0.3164	-0.0961	0.0696	0.2195	-0.0608	0.253	-4.2348	120.2365	149.5117
13	0.148	-0.1042	-0.0414	0.1321	0.1213	0.5244	0.1452	-0.1892	0.039	0.0639	0.109	-0.0193	-0.3061	-0.0178	0.3322	0.2014	-0.036	-0.01	0.3023	0.0127	0.1014	-9.9792	109.6499	170.7419
14	0.0347	0.0928	-0.1185	0.3099	-0.3319	0.4466	0.0185	-0.4723	0.3862	-0.2771	-0.1811	0.2434	0.1113	-0.1879	-0.1774	0.2542	0.0664	-0.1363	0.4273	-0.2114	0.4511	-33.1268	112.6405	176.1158
15	0.2162	0.0347	0.2554	0.3347	0.1776	0.2882	0.1735	-0.3427	0.1136	-0.0463	0.0283	-0.1702	0.1401	0.0062	-0.0018	0.0545	-0.045	-0.0742	0.539	-0.0869	0.2162	-6.8214	99.4401	174.9799
16	0.1882	-0.0233	0.0201	0.0334	0.042	0.1437	-0.073	-0.25	-0.1985	-0.0208	-0.0902	0.0691	0.0031	0.1044	-0.2238	0.0672	0.0189	-0.0729	0.1163	0.1664	-0.1567	-18.5934	83.9988	147.3568
17	0.1328	0.0643	0.0959	0.3104	0.1504	0.075	0.0296	-0.0397	-0.1253	-0.0483	0.0643	0.1173	0.0662	-0.216	0.0325	0.0881	0.0521	-0.0113	0.3799	0.1095	0.1995	-29.8063	91.062	139.5401
18	0.0234	0.0095	0.0408	0.0841	0.0543	0.0666	-0.0843	-0.0149	-0.1369	-0.0805	0.0307	-0.0218	-0.0692	-0.0544	-0.0072	0.2967	0.0615	0.0133	0.3156	0.0526	0.2701	-24.1471	98.261	135.5833
19	0.0878	-0.0001	-0.0613	0.0555	0.0141	0.0237	0.067	0.1707	0.104	-0.1657	0.0552	0.0141	-0.2572	-0.0955	0.1658	0.3545	0.0576	0.0608	0.1795	0.0768	0.2124	-18.0537	117.0784	134.5498

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 264 )	A	1 - 264
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 265 through 703 )	A	265 - 703
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 704 through 1280 )	A	704 - 1280
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 291 )	B	1 - 291
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 292 through 478 )	B	292 - 478
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 479 through 649 )	B	479 - 649
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 650 through 1280 )	B	650 - 1280
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 1 through 264 )	C	1 - 264
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 265 through 744 )	C	265 - 744
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 745 through 1280 )	C	745 - 1280
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 1 through 95 )	D	1 - 95
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 96 through 202 )	D	96 - 202
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 203 through 332 )	D	203 - 332
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 333 through 478 )	D	333 - 478
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 479 through 675 )	D	479 - 675
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 676 through 870 )	D	676 - 870
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 871 through 997 )	D	871 - 997
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 998 through 1099 )	D	998 - 1099
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1100 through 1280 )	D	0

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