PDB-8zr8: The Crystal Structure of Nudix Hydrolase from Bacillus methanolicus C1

ID or keywords:

Entry

Database: PDB / ID: 8zr8

Title

The Crystal Structure of Nudix Hydrolase from Bacillus methanolicus C1

Components

Methanol dehydrogenase activator

Keywords

HYDROLASE / Nudix Hydrolase

Function / homology

Function and homology information

Hydrolases / nucleoside phosphate metabolic process / ribose phosphate metabolic process / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / hydrolase activity / magnesium ion binding / cytosol
Similarity search - Function

Biological species

Bacillus methanolicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.11 Å

Authors

Chen, C.Y. / Huang, C.H.

Funding support

1items

Citation

Journal: To Be Published
Title: The Crystal Structure of Nudix Hydrolase from Bacillus methanolicus C1
Authors: Chen, C.Y. / Huang, C.H.

History

Deposition	Jun 4, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 4, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8zr8.cif.gz	222.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8zr8.ent.gz	180.9 KB	Display	PDB format
PDBx/mmJSON format	8zr8.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/zr/8zr8 ftp://data.pdbj.org/pub/pdb/validation_reports/zr/8zr8	HTTPS FTP

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Related structure data

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	#145 - Jan 2012 Messenger RNA Capping similarity (6) #201 - Sep 2016 Isoprene Synthase similarity (4)

Deposited unit

A: Methanol dehydrogenase activator

B: Methanol dehydrogenase activator

C: Methanol dehydrogenase activator

65.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Methanol dehydrogenase activator

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

2

B: Methanol dehydrogenase activator

C: Methanol dehydrogenase activator

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

Unit cell

Length a, b, c (Å)	55.993, 106.657, 194.911
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Methanol dehydrogenase activator / Nudix Hydrolase / MDH activator Mass: 21732.822 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus methanolicus (bacteria) / Gene: act / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KP10
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H₂O
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: 2.3 Å³/Da / Density % sol: 46.63 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1M Tris pH 8.0, 30% w/v Polyethylene glycol monomethyl ether 2000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 15, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979183 Å / Relative weight: 1
Reflection	Resolution: 2.11→34.75 Å / Num. obs: 34081 / % possible obs: 99.76 % / Redundancy: 12.3 % / CC_1/2: 0.994 / R_merge(I) obs: 0.151 / R_pim(I) all: 0.04498 / R_rim(I) all: 0.158 / Net I/σ(I): 8.27
Reflection shell	Resolution: 2.11→2.185 Å / R_merge(I) obs: 1.264 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 3356 / CC_1/2: 0.725 / R_pim(I) all: 0.4116

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.11→34.75 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2688	1613	4.74 %
R_work	0.2246	-	-
obs	0.2268	34022	99.77 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.11→34.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4122	0	0	112	4234

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015
X-RAY DIFFRACTION	f_angle_d	1.63
X-RAY DIFFRACTION	f_dihedral_angle_d	6.996	545
X-RAY DIFFRACTION	f_chiral_restr	0.105	654
X-RAY DIFFRACTION	f_plane_restr	0.011	718

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.11-2.17	0.3262	114	0.3012	2678	X-RAY DIFFRACTION	99
2.17-2.24	0.3275	138	0.2807	2665	X-RAY DIFFRACTION	100
2.24-2.32	0.322	98	0.2786	2691	X-RAY DIFFRACTION	100
2.32-2.42	0.3458	132	0.2994	2681	X-RAY DIFFRACTION	100
2.42-2.52	0.3964	119	0.2946	2658	X-RAY DIFFRACTION	100
2.53-2.66	0.3854	144	0.276	2663	X-RAY DIFFRACTION	100
2.66-2.82	0.3169	168	0.2703	2660	X-RAY DIFFRACTION	100
2.82-3.04	0.3072	133	0.2792	2691	X-RAY DIFFRACTION	100
3.04-3.35	0.2912	167	0.2452	2683	X-RAY DIFFRACTION	100
3.35-3.83	0.2429	127	0.2106	2720	X-RAY DIFFRACTION	100
3.83-4.83	0.2147	143	0.1753	2733	X-RAY DIFFRACTION	100
4.83-34.75	0.2243	130	0.1866	2886	X-RAY DIFFRACTION	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	1.9756	-0.8919	1.1569	0.8757	-0.9268	0.7067	-0.1445	0.6465	-0.3532	0.0433	-0.0063	0.604	0.2597	-0.6549	0.0002	0.6181	0.0838	0.073	0.6822	-0.1227	0.494	-21.3749	-24.3832	-38.7137
2	3.8498	-0.6963	-0.0661	2.3128	2.8824	3.9994	-0.018	0.5816	0.4103	-0.2783	0.3989	-0.3273	-0.8792	0.155	0.0025	0.2886	-0.0543	0.0727	0.46	0.0669	0.5154	-3.0357	6.8943	-9.4353
3	3.1662	-0.5777	2.3409	3.4252	0.9918	3.6808	0.2266	-0.0507	-0.404	0.0089	-0.2373	-0.0458	0.4997	-0.0694	0.0024	0.2616	-0.021	-0.0307	0.3178	0.0019	0.433	-21.6418	-12.5424	1.278
4	1.2127	1.0475	-0.9888	0.9509	-0.8921	0.8938	0.2422	0.0316	-1.5724	0.3948	-0.8846	-1.2818	1.3791	0.3794	-0.2021	0.7482	0.0928	-0.2334	0.4423	-0.0496	0.6309	-22.4968	-19.6611	-6.6924
5	1.597	-0.6917	0.6869	2.7198	-0.4143	4.1333	0.4539	-0.127	-0.6104	0.0098	-0.3807	-0.0021	0.8287	-0.2187	0.0018	0.3296	-0.0212	-0.0392	0.3276	-0.0173	0.4472	-25.502	-12.6044	-5.1503
6	1.1929	-0.4254	0.8812	1.2244	-0.3127	2.1997	0.0721	-0.3357	-0.2134	0.9904	-0.2878	0.4472	0.7447	-0.3223	-0.0054	0.3416	-0.1442	0.1131	0.5471	0.0535	0.4161	-30.4597	-8.8811	11.0421
7	0.089	-0.2195	0.2245	0.954	-0.2928	0.6517	0.0413	1.0504	-0.095	0.493	-0.3826	0.4533	0.051	-0.5384	-0.0402	0.1993	-0.0549	0.0152	0.5031	-0.0743	0.4261	-34.0379	-4.8419	0.6196
8	0.8507	-1.1992	1.2234	1.4706	-1.7957	4.7579	0.1073	1.1706	-0.3832	0.2536	-0.7572	-0.0619	-1.6892	1.3382	-0.0431	0.2851	-0.0364	0.0025	0.9872	-0.1676	0.6219	-49.7267	-0.0233	-10.91
9	0.6117	0.093	-0.1273	0.3197	0.3075	0.2214	1.0424	1.5654	-0.2689	0.2074	-0.5518	-0.3189	-0.5611	0.7814	0.001	1.2258	-0.0206	-0.225	0.5988	0.0943	0.8811	-7.9928	2.9834	-45.4184
10	2.9555	-0.1048	-0.2462	0.9509	0.4151	0.8616	-0.2567	0.5979	1.9002	0.1794	-0.677	-0.619	-0.4049	0.818	-0.0103	1.1141	0.1694	-0.1351	0.6398	0.0131	0.4993	-0.4713	-0.5448	-36.9172
11	2.6728	-0.7702	-0.0269	3.5047	0.852	2.3189	-0.2665	0.0638	0.0413	0.7439	-0.0008	-0.7313	-0.1522	-0.0462	-0.0013	0.6341	0.1184	-0.0736	0.3531	0.0163	0.4181	-1.1642	-20.0888	-34.2042
12	2.0254	-0.1603	0.3332	1.745	-0.5955	5.2359	-0.3555	-0.1125	-0.3399	0.5991	0.1247	-0.1353	0.3142	0.0144	-0.0002	0.5647	0.1277	0.0122	0.3648	0.003	0.4689	-4.3955	-28.1897	-31.6694
13	0.4791	-0.1053	0.0282	0.089	-0.069	0.3143	-0.5307	-0.3993	-0.8113	-0.5745	0.3426	-0.3887	-0.0114	-0.9947	0.0036	0.6386	0.0368	0.1244	0.5972	-0.0769	0.4839	-13.5582	-31.3432	-32.4329
14	2.0986	1.6102	-0.4817	1.9067	0.8342	1.8004	1.0539	0.1318	-0.3462	0.136	-0.3027	0.5714	0.8366	1.6159	0.0503	0.914	0.3629	-0.2298	0.7994	-0.1042	0.4287	4.7324	-5.7353	-21.5388
15	2.1142	-0.0463	-0.508	2.8804	-0.7488	1.6123	-0.3744	0.6441	0.3542	0.5377	0.4584	0.4914	-0.1852	-0.6636	0.0097	0.7848	0.28	0.0139	0.6204	0.0023	0.4671	-21.0787	-10.8596	-33.6476
16	0.8191	0.7264	0.659	3.2077	0.1953	1.9992	0.1611	0.4204	0.009	1.3272	-0.0162	0.5893	-0.6352	-0.8298	0.0004	1.1407	0.3654	0.1892	0.6479	0.0255	0.5145	-22.6318	-13.5554	-25.0153
17	0.4264	0.4677	0.4964	0.4762	0.5991	0.6462	-0.4703	0.2989	0.2324	0.9115	2.143	1.9198	-0.7833	-0.3673	0.2108	0.6702	0.4028	0.2731	0.8736	0.0714	0.7202	-31.714	-13.3969	-37.5245

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 152 through 184 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 5 through 42 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 43 through 85 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 86 through 98 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 99 through 146 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 147 through 166 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 167 through 181 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 182 through 190 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 5 through 14 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 15 through 29 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 30 through 98 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 99 through 166 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 167 through 182 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 6 through 42 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 43 through 85 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 86 through 128 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 129 through 151 )

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