PDB-9d6j: Nitrile hydratase BR52K mutant

ID or keywords:

Entry

Database: PDB / ID: 9d6j

Title

Nitrile hydratase BR52K mutant

Components

Cobalt-containing nitrile hydratase subunit alpha
Cobalt-containing nitrile hydratase subunit beta

Keywords

LYASE / nitrile hydratase

Function / homology

Function and homology information

nitrile catabolic process / nitrile hydratase / nitrile hydratase activity / cobalt ion binding / transition metal ion binding
Similarity search - Function

Biological species

Pseudonocardia thermophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.47 Å

Authors

Miller, C.G. / Holz, R.C. / Liu, D. / Kaley, N.

Funding support

United States, 1items

Citation

Journal: J Inorg Biochem / Year: 2024
Title: Role of second-sphere arginine residues in metal binding and metallocentre assembly in nitrile hydratases.
Authors: Miller, C. / Huntoon, D. / Kaley, N. / Ogutu, I. / Fiedler, A.T. / Bennett, B. / Liu, D. / Holz, R.

History

Deposition	Aug 15, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 28, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9d6j.cif.gz	204.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9d6j.ent.gz	164.4 KB	Display	PDB format
PDBx/mmJSON format	9d6j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9d6j_validation.pdf.gz	433 KB	Display	wwPDB validaton report
Full document	9d6j_full_validation.pdf.gz	435.6 KB	Display
Data in XML	9d6j_validation.xml.gz	23.1 KB	Display
Data in CIF	9d6j_validation.cif.gz	35.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d6/9d6j ftp://data.pdbj.org/pub/pdb/validation_reports/d6/9d6j	HTTPS FTP

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Related structure data

Related structure data	9d65C 9d6kC 9d6mC 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	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #66 - Jun 2005 Carotenoid Oxygenase similarity (1)

Deposited unit

A: Cobalt-containing nitrile hydratase subunit alpha

B: Cobalt-containing nitrile hydratase subunit beta

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

1

Idetical with deposited unit
defined by author&software
Evidence: native gel electrophoresis

Unit cell

Length a, b, c (Å)	65.895, 65.895, 184.943
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	B-575- HOH

#1: Protein	Cobalt-containing nitrile hydratase subunit alpha / L-NHase / L-nitrilase Mass: 23171.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudonocardia thermophila (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q7SID2, nitrile hydratase
#2: Protein	Cobalt-containing nitrile hydratase subunit beta / L-NHase / L-nitrilase Mass: 26142.133 Da / Num. of mol.: 1 / Mutation: R52K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudonocardia thermophila (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q7SID3, nitrile hydratase
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.67 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1.2 M sodium citrate tribasic in 0.1 M HEPES at pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MAR CCD 300 mm / Detector: CCD / Date: Nov 10, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.47→19.55 Å / Num. obs: 79376 / % possible obs: 98.9 % / Redundancy: 10.8 % / R_merge(I) obs: 0.066 / R_pim(I) all: 0.021 / R_rim(I) all: 0.069 / Net I/σ(I): 18.4
Reflection shell	Resolution: 1.47→1.494 Å / Redundancy: 11 % / R_merge(I) obs: 0.932 / Num. unique obs: 3868 / R_pim(I) all: 0.291 / R_rim(I) all: 0.977

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_5156: ???)	refinement
SCALA		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.47→19.55 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2279	4006	5.05 %
R_work	0.1955	-	-
obs	0.1972	79375	98.85 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.47→19.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3460	0	0	550	4010

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004
X-RAY DIFFRACTION	f_angle_d	0.741
X-RAY DIFFRACTION	f_dihedral_angle_d	17.117	1355
X-RAY DIFFRACTION	f_chiral_restr	0.079	511
X-RAY DIFFRACTION	f_plane_restr	0.008	652

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 (%)
1.47-1.49	0.3251	172	0.2803	2495	X-RAY DIFFRACTION	98
1.49-1.5	0.2867	143	0.2535	2536	X-RAY DIFFRACTION	98
1.5-1.52	0.2811	126	0.2636	2532	X-RAY DIFFRACTION	98
1.52-1.54	0.3086	131	0.2565	2554	X-RAY DIFFRACTION	98
1.54-1.56	0.2782	155	0.2375	2571	X-RAY DIFFRACTION	99
1.56-1.59	0.276	159	0.2253	2523	X-RAY DIFFRACTION	98
1.59-1.61	0.2599	133	0.224	2578	X-RAY DIFFRACTION	99
1.61-1.64	0.2404	152	0.2218	2501	X-RAY DIFFRACTION	99
1.64-1.66	0.2464	91	0.2201	2603	X-RAY DIFFRACTION	99
1.66-1.69	0.2537	136	0.2181	2613	X-RAY DIFFRACTION	99
1.69-1.72	0.263	165	0.2152	2519	X-RAY DIFFRACTION	99
1.72-1.76	0.2318	114	0.2199	2602	X-RAY DIFFRACTION	99
1.76-1.79	0.2771	138	0.2111	2584	X-RAY DIFFRACTION	99
1.79-1.83	0.2241	123	0.2033	2608	X-RAY DIFFRACTION	99
1.83-1.87	0.2176	132	0.2047	2584	X-RAY DIFFRACTION	99
1.87-1.92	0.213	148	0.2053	2570	X-RAY DIFFRACTION	99
1.92-1.97	0.2374	139	0.2083	2599	X-RAY DIFFRACTION	99
1.97-2.03	0.2404	125	0.1995	2596	X-RAY DIFFRACTION	99
2.03-2.09	0.2237	139	0.1926	2594	X-RAY DIFFRACTION	99
2.09-2.17	0.2185	157	0.1892	2595	X-RAY DIFFRACTION	99
2.17-2.26	0.2235	135	0.1894	2643	X-RAY DIFFRACTION	99
2.26-2.36	0.2091	136	0.1867	2648	X-RAY DIFFRACTION	100
2.36-2.48	0.2327	134	0.1906	2630	X-RAY DIFFRACTION	100
2.48-2.64	0.241	156	0.1919	2644	X-RAY DIFFRACTION	100
2.64-2.84	0.2241	125	0.1932	2651	X-RAY DIFFRACTION	100
2.84-3.13	0.2125	120	0.202	2704	X-RAY DIFFRACTION	100
3.13-3.57	0.2384	122	0.1788	2495	X-RAY DIFFRACTION	93
3.58-4.49	0.1816	125	0.1716	2749	X-RAY DIFFRACTION	100
4.5-10	0.2281	175	0.1942	2848	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	0.9094	0.0639	0.7106	0.808	-0.2677	2.9662	-0.1524	0.095	0.0306	-0.0348	0.0257	-0.0317	-0.326	0.2534	-0.014	0.2056	-0.04	-0.0398	0.1386	0.0231	0.1863	-36.8626	44.4164	11.2727
2	0.1759	-0.1545	-0.3526	2.0877	0.5542	0.6772	-0.0153	-0.1279	-0.0794	-0.0323	0.0687	-0.2247	-0.0596	0.0977	0.0191	0.2275	0.0047	-0.0569	0.1696	0.0403	0.1984	-27.5166	23.9565	25.1181
3	0.9478	-0.4427	-0.0717	1.8376	-0.1327	0.5351	-0.0713	-0.1222	-0.2546	0.2218	-0.119	-0.0982	0.1574	-0.0485	0.0431	0.2787	0.0316	0.0016	0.1543	0.0361	0.2611	-32.1847	7.0628	25.7795
4	1.9056	0.6715	0.2196	0.4735	-0.6496	2.1017	-0.1412	0.0235	-0.0943	0.0318	0.0567	-0.0248	0.0655	-0.016	0.0392	0.3025	-0.0092	-0.0239	0.1309	0.0185	0.2292	-36.2888	11.1733	11.9003
5	1.6693	-0.0985	-0.1109	1.4874	-0.4312	0.8393	-0.0204	0.3324	-0.072	-0.2159	-0.0202	-0.0616	0.2252	0.0914	0.0255	0.2634	0.0113	-0.0234	0.1681	0.0069	0.1686	-34.9211	15.5346	4.0369
6	2.3348	0.0191	-0.102	0.8955	-0.1176	1.0198	0.1592	0.361	0.1093	0.0303	-0.1912	-0.2019	0.1235	-0.0224	0.0493	0.27	0.0124	-0.0081	0.1696	0.036	0.2155	-29.4162	8.0036	14.8058
7	2.6156	-0.6219	0.6656	1.7163	-0.4685	1.736	-0.0038	0.0006	0.0358	0.0989	-0.1166	-0.4628	-0.0873	0.182	0.08	0.2637	0.015	-0.0384	0.1685	0.0383	0.3268	-21.3566	11.5808	11.7922
8	0.3567	0.17	0.3473	1.2562	0.1375	1.0581	-0.2321	0.2584	0.2339	-0.1729	0.1982	-0.0144	-0.0527	0.1167	-0.0031	0.222	-0.0393	-0.0175	0.1488	0.033	0.1719	-37.2606	27.0987	5.0679
9	1.9713	0.3488	-1.8792	1.153	-0.5994	2.6675	0.0755	-0.1474	0.029	0.1554	-0.0009	-0.1262	0.1294	-0.0875	0.0396	0.2569	-0.0101	-0.056	0.1442	0.0245	0.1969	-36.5427	34.8374	23.587
10	0.7009	0.4512	-0.1313	0.9665	0.1222	2.3787	-0.0286	0.0404	0.0901	0.2835	0.1679	0.2089	0.0471	-0.0935	-0.0168	0.2404	-0.0527	-0.01	0.1364	0.0703	0.1814	-48.9132	30.393	20.1682
11	0.707	0.228	0.1446	0.8643	0.1111	1.0162	0.0373	0.0917	0.0509	0.0732	0.0659	0.119	-0.0224	-0.03	-0.0131	0.2093	-0.0182	-0.0233	0.1456	0.0336	0.1755	-44.2702	35.9749	13.5226
12	2.6967	1.5401	-1.0444	1.7586	-0.8269	1.4001	0.1727	-0.2607	0.81	0.2001	-0.0552	0.4858	-0.3315	-0.1275	-0.0795	0.2971	0.0303	-0.0083	0.1626	0.015	0.2857	-43.721	50.7772	21.2232
13	1.0185	0.0766	-0.0817	3.1222	-2.2317	3.5618	0.0687	-0.2651	0.188	0.4154	0.0269	0.1988	-0.5136	0.1179	-0.0269	0.3073	0.0063	-0.0361	0.1797	-0.0047	0.1882	-32.0869	48.4253	29.8467
14	1.584	0.1429	0.4744	4.4911	1.8055	1.812	-0.0104	-0.3071	-0.122	0.4179	0.0066	0.1447	0.2867	-0.1293	0.0465	0.2198	-0.0183	-0.029	0.2298	0.0652	0.1627	-33.8951	28.5309	34.973
15	1.0058	0.7688	-0.2553	1.522	0.3121	1.5902	-0.002	-0.1556	-0.172	0.0992	-0.0415	0.0514	0.1288	-0.1758	-0.0126	0.2531	-0.0163	-0.0175	0.1388	0.0229	0.2016	-53.6506	7.2429	21.6284
16	1.1974	0.0516	-0.0921	1.0934	0.0532	1.7964	-0.0995	0.0743	0.048	-0.0694	0.0303	0.0205	-0.0109	-0.0538	-0.0193	0.228	-0.0299	-0.0348	0.1519	0.0198	0.2024	-54.4391	14.5572	9.8629
17	0.9392	-0.3399	0.1565	0.8998	-0.4935	0.9076	-0.0301	0.0428	-0.0875	0.0109	0.124	0.0707	0.1536	0.0036	-0.0209	0.204	-0.0443	-0.016	0.1506	0.023	0.1853	-51.9533	13.0097	14.1476
18	1.7128	-0.9182	-0.4295	0.8253	0.058	1.7072	-0.0141	0.171	-0.3743	0.0106	0.0538	0.1088	0.3841	-0.1203	-0.0147	0.2932	-0.0612	-0.0286	0.1582	-0.0122	0.2643	-51.0537	6.7936	9.0824

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 30 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 31 through 64 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 65 through 92 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 93 through 115 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 116 through 161 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 162 through 182 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 183 through 204 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 27 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 28 through 42 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 43 through 57 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 58 through 82 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 83 through 100 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 101 through 112 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 113 through 125 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 126 through 147 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 148 through 172 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 173 through 207 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 208 through 228 )

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