PDB-7hk9: Crystal Structure of N-methylhydantoinase in complex with ZN2+ an...

ID or keywords:

Entry

Database: PDB / ID: 7hk9

Title

Crystal Structure of N-methylhydantoinase in complex with ZN2+ and ADPNP

Components

N-methylhydantoinase

Keywords

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

Function / homology

ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMMONIUM ION

Function and homology information

Biological species

Glutamicibacter protophormiae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.58 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	7hk9.cif.gz	999.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7hk9.ent.gz	823.2 KB	Display	PDB format
PDBx/mmJSON format	7hk9.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/7hk9 ftp://data.pdbj.org/pub/pdb/validation_reports/hk/7hk9	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

hetero molecules

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

1

B: N-methylhydantoinase

hetero molecules

A: N-methylhydantoinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.841, 184.988, 289.013
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	(chain A and (resid 1 through 1280 or resid 1303 through 1312 or resid 1444))
2	1	(chain B and (resid 1 through 1280 or resid 1301 through 1310 or resid 1444))

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	ALA	ALA	(chain A and (resid 1 through 1280 or resid 1303 through 1312 or resid 1444))	A	A	1 - 1280	1 - 1280
1	2	ZN	ZN	ZN	ZN	(chain A and (resid 1 through 1280 or resid 1303 through 1312 or resid 1444))	A	F - O	1304 - 1313
1	3	ACT	ACT	ACT	ACT	(chain A and (resid 1 through 1280 or resid 1303 through 1312 or resid 1444))	A	Q	1315
2	1	MET	MET	ALA	ALA	(chain B and (resid 1 through 1280 or resid 1301 through 1310 or resid 1444))	B	B	1 - 1280	1 - 1280
2	2	ZN	ZN	ZN	ZN	(chain B and (resid 1 through 1280 or resid 1301 through 1310 or resid 1444))	B	S - BA	1302 - 1311
2	3	ACT	ACT	ACT	ACT	(chain B and (resid 1 through 1280 or resid 1301 through 1310 or resid 1444))	B	DA	1313

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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 , 5 types, 563 molecules

#2: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical	... ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NH4 / AMMONIUM ION Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₄N
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 535 / 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: 3.57 Å³/Da / Density % sol: 65.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20.8 mg/ml protein in 20mM HEPES/NaOH pH 7.4, 0.1 M NaCl, 100 mM MgCl2, 30mM NH4Cl mixed 1+1 with 0.050 M zinc chloride, 5 %w/v PEG 3350, 0.75 M ammonium acetate, 0.1 M Bis-Tris/HCl pH 5.5 ...Details: 20.8 mg/ml protein in 20mM HEPES/NaOH pH 7.4, 0.1 M NaCl, 100 mM MgCl2, 30mM NH4Cl mixed 1+1 with 0.050 M zinc chloride, 5 %w/v PEG 3350, 0.75 M ammonium acetate, 0.1 M Bis-Tris/HCl pH 5.5 plus 15x and 3x molar excess of ADPNP and DHU

Crystal

Density Matthews: 3.57 Å³/Da / Density % sol: 65.54 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20.8 mg/ml protein in 20mM HEPES/NaOH pH 7.4, 0.1 M NaCl, 100 mM MgCl2, 30mM NH4Cl mixed 1+1 with 0.050 M zinc chloride, 5 %w/v PEG 3350, 0.75 M ammonium acetate, 0.1 M Bis-Tris/HCl pH 5.5 ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 0.99989 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.99989 Å / Relative weight: 1

Reflection

Resolution: 2.58→77.9 Å / Num. obs: 127176 / % possible obs: 99.9 % / Redundancy: 6.835 % / B_iso Wilson estimate: 59.22 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.089 / R_rim(I) all: 0.096 / Χ²: 0.854 / Net I/σ(I): 12.31 / Num. measured all: 869307 / Scaling rejects: 67

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
2.58-2.65	6.96	2.733	0.64	64293	9243	9238	0.387	2.954	99.9
2.65-2.72	6.802	2.113	0.87	61546	9054	9048	0.501	2.289	99.9
2.72-2.8	6.443	1.473	1.21	56941	8843	8838	0.67	1.605	99.9
2.8-2.88	6.683	1.145	1.67	57518	8611	8607	0.762	1.243	100
2.88-2.98	7.137	0.874	2.31	59250	8302	8302	0.856	0.942	100
2.98-3.08	7.231	0.64	3.18	58006	8025	8022	0.92	0.69	100
3.08-3.2	7.202	0.447	4.42	56022	7781	7779	0.96	0.482	100
3.2-3.33	7.116	0.33	5.93	53288	7494	7488	0.975	0.356	99.9
3.33-3.48	7.048	0.215	8.58	50672	7192	7190	0.989	0.232	100
3.48-3.65	6.918	0.152	11.56	47613	6882	6882	0.994	0.164	100
3.65-3.85	6.758	0.117	14.49	44508	6589	6586	0.995	0.127	100
3.85-4.08	6.272	0.083	18.37	39091	6234	6233	0.997	0.09	100
4.08-4.36	6.56	0.067	23.16	38440	5862	5860	0.998	0.073	100
4.36-4.71	7.068	0.058	28.49	38817	5492	5492	0.998	0.062	100
4.71-5.16	7.032	0.053	30.08	35498	5050	5048	0.999	0.058	100
5.16-5.77	6.908	0.052	30.53	32012	4635	4634	0.998	0.056	100
5.77-6.66	6.669	0.048	31.4	27104	4066	4064	0.999	0.052	100
6.66-8.16	6.036	0.036	37.45	21036	3494	3485	0.999	0.039	99.7
8.16-11.54	6.445	0.027	47.27	17776	2762	2758	0.999	0.029	99.9
11.54-57.04	6.089	0.023	47.96	9876	1640	1622	1	0.025	98.9

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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: 2.58→57.04 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.26 / Stereochemistry target values: ML
Details: failed soak with DHU and ADPNP - only ADPNP visible in electron density. A number of Zn2+ sites are apparent, many with occupancy less than one. Zn2+ has replaced both the Ca2+ at the NMH ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2255	4829	4.96 %	RANDOM
R_work	0.194	92594	-	-
obs	0.1955	97423	76.64 %	-

Solvent computation

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

Displacement parameters

B_iso max: 220.12 Å² / B_iso mean: 72.7561 Å² / B_iso min: 23.32 Å²

Refinement step

Cycle: final / Resolution: 2.58→57.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19629	0	94	535	20258
B_iso mean	-	-	79.92	56.13	-
Num. residues	-	-	-	-	2567

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	12218	X-RAY DIFFRACTION	5.789	TORSIONAL
1	2	B	12218	X-RAY DIFFRACTION	5.789	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 (%)
2.58-2.61	0.3793	36	0.3532	627	663	16
2.61-2.64	0.3173	40	0.3254	792	832	20
2.64-2.67	0.342	51	0.3136	954	1005	24
2.67-2.71	0.3827	57	0.3096	1151	1208	29
2.71-2.74	0.3112	65	0.2953	1415	1480	35
2.74-2.78	0.3232	83	0.2849	1572	1655	39
2.78-2.82	0.3477	112	0.2919	1878	1990	48
2.82-2.86	0.3159	124	0.2919	2228	2352	56
2.86-2.91	0.3397	127	0.2854	2450	2577	61
2.91-2.95	0.3169	131	0.2799	2643	2774	66
2.95-3	0.3323	134	0.2814	2842	2976	71
3-3.06	0.3036	160	0.2945	2965	3125	75
3.06-3.12	0.3711	149	0.312	3285	3434	81
3.12-3.18	0.293	169	0.2678	3436	3605	87
3.18-3.25	0.2964	199	0.2521	3666	3865	91
3.25-3.33	0.2859	201	0.2423	3745	3946	95
3.33-3.41	0.2907	218	0.222	3973	4191	99
3.41-3.5	0.2659	228	0.2187	3983	4211	100
3.5-3.6	0.2397	212	0.2058	3985	4197	100
3.6-3.72	0.2254	214	0.1987	4019	4233	100
3.72-3.85	0.2335	204	0.1997	4039	4243	100
3.85-4.01	0.2051	219	0.1716	4006	4225	100
4.01-4.19	0.1712	186	0.1617	4085	4271	100
4.19-4.41	0.171	228	0.1495	4057	4285	100
4.41-4.69	0.1803	222	0.1456	4032	4254	100
4.69-5.05	0.1686	193	0.1483	4069	4262	100
5.05-5.56	0.187	227	0.1622	4068	4295	100
5.56-6.36	0.2429	222	0.1926	4107	4329	100
6.36-8.01	0.1904	210	0.1853	4169	4379	100
8.01-57.04	0.1981	208	0.1666	4353	4561	99

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	0.0188	0.032	0.0022	0.0607	-0.0167	0.0222	0.0799	-0.2557	-0.192	0.1072	-0.0741	-0.1227	0.2343	0.0082	-0.0292	0.4699	-0.0325	-0.009	0.542	0.1778	0.3469	17.4053	10.9727	32.5695
2	0.015	-0.0153	-0.0115	0.0174	-0.0087	0.0309	-0.0055	-0.0621	0.037	0.0408	-0.0259	-0.0672	-0.0228	0.0141	-0	0.3178	-0.0882	-0.0204	0.4662	0.0037	0.3372	10.492	33.0326	31.1344
3	0.0721	-0.02	0.0466	0.0034	-0.0142	0.0422	-0.0527	-0.1574	-0.0461	0.0592	-0.0786	-0.0175	0.151	-0.0845	-0.039	0.4864	-0.1215	0.1115	0.4089	0.1007	0.4129	-0.0049	15.2879	24.6966
4	0.038	-0.0012	-0.018	0.0221	-0.0313	0.0397	-0.0384	-0.1888	0.0106	0.0112	0.0476	0.0461	0.01	-0.1777	0	0.5719	-0.0567	0.1132	0.5198	-0.0539	0.5093	-4.9472	27.791	28.4142
5	0.1587	0.0795	-0.1523	0.0798	0.0023	0.295	-0.0695	0.0139	-0.0901	0.0403	0.0088	-0.0338	0.0755	0.0017	-0.0016	0.3298	-0.0034	0.0398	0.3322	0.0194	0.3344	21.7278	18.447	-2.4833
6	0.0027	0.0042	-0.0126	0.0207	0.033	0.1243	-0.0301	0.157	-0.1114	-0.0255	-0.185	0.0142	0.0143	-0.0476	-0.2197	0.5722	-0.2133	0.4029	0.9977	-0.6557	0.523	14.894	-11.6601	-72.407
7	0.0092	0.01	-0.0078	0.0358	-0.0246	0.1262	-0.0984	0.0574	-0.0825	-0.0073	-0.0078	0.0061	-0.0699	-0.2291	-0.0392	0.6781	-0.2809	0.3018	0.8258	-0.5995	0.581	-0.7676	-21.2537	-69.7154
8	0.0766	-0.02	0.0515	0.2004	-0.041	0.1353	-0.2043	0.1848	-0.2051	0.0584	-0.1273	-0.0714	0.3462	-0.1487	-0.4448	0.6673	-0.2212	0.4529	0.3577	-0.519	0.6564	18.6285	-18.0393	-37.4724

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 414 )	A	265 - 414
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 415 through 564 )	A	415 - 564
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 565 through 684 )	A	565 - 684
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 685 through 1287 )	A	685 - 1287
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 313 )	B	1 - 313
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 314 through 702 )	B	314 - 702
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 703 through 1280 )	B	703 - 1280

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