PDB-9d6m: Nitrile hydratase BR157K mutant

ID or keywords:

Entry

Database: PDB / ID: 9d6m

Title

Nitrile hydratase BR157K 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 activity / nitrile hydratase / indole-3-acetonitrile 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: 1.56 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
Revision 1.1	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9d6m.cif.gz	203.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9d6m.ent.gz	161.5 KB	Display	PDB format
PDBx/mmJSON format	9d6m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9d6m_validation.pdf.gz	427 KB	Display	wwPDB validaton report
Full document	9d6m_full_validation.pdf.gz	430.3 KB	Display
Data in XML	9d6m_validation.xml.gz	24.6 KB	Display
Data in CIF	9d6m_validation.cif.gz	38.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d6/9d6m ftp://data.pdbj.org/pub/pdb/validation_reports/d6/9d6m	HTTPS FTP

-
Related structure data

Related structure data	9d65C 9d6jC 9d6kC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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)	65.910, 65.910, 184.280
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-607- 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: 26142.135 Da / Num. of mol.: 1 / Mutation: R157K 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.: 670 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.51 %
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

-
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: 1.56→19.54 Å / Num. obs: 67530 / % possible obs: 100 % / Redundancy: 13.1 % / R_merge(I) obs: 0.067 / R_pim(I) all: 0.019 / R_rim(I) all: 0.07 / Net I/σ(I): 20.6
Reflection shell	Resolution: 1.56→1.583 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.737 / Num. unique obs: 3352 / R_pim(I) all: 0.286 / R_rim(I) all: 0.793

-
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: 1.56→19.54 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1913	3422	5.07 %
R_work	0.1694	-	-
obs	0.1705	67530	99.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.56→19.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3463	0	0	670	4133

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005
X-RAY DIFFRACTION	f_angle_d	0.828
X-RAY DIFFRACTION	f_dihedral_angle_d	16.177	1363
X-RAY DIFFRACTION	f_chiral_restr	0.051	512
X-RAY DIFFRACTION	f_plane_restr	0.008	649

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 (%)
1.56-1.58	0.278	141	0.2403	2622	X-RAY DIFFRACTION	99
1.58-1.6	0.2576	144	0.2261	2636	X-RAY DIFFRACTION	100
1.6-1.63	0.2333	160	0.2124	2598	X-RAY DIFFRACTION	100
1.63-1.65	0.2611	153	0.2047	2634	X-RAY DIFFRACTION	100
1.65-1.68	0.2523	109	0.2041	2662	X-RAY DIFFRACTION	100
1.68-1.71	0.1936	137	0.1928	2619	X-RAY DIFFRACTION	100
1.71-1.75	0.2137	152	0.1958	2649	X-RAY DIFFRACTION	100
1.75-1.78	0.2144	139	0.1921	2660	X-RAY DIFFRACTION	100
1.78-1.82	0.2066	153	0.1909	2600	X-RAY DIFFRACTION	100
1.82-1.86	0.2152	119	0.1838	2656	X-RAY DIFFRACTION	100
1.86-1.91	0.23	139	0.1823	2646	X-RAY DIFFRACTION	100
1.91-1.96	0.1952	150	0.1835	2656	X-RAY DIFFRACTION	100
1.96-2.02	0.2201	152	0.1725	2639	X-RAY DIFFRACTION	100
2.02-2.08	0.2089	173	0.1723	2623	X-RAY DIFFRACTION	100
2.08-2.16	0.1849	132	0.1697	2686	X-RAY DIFFRACTION	100
2.16-2.24	0.1902	128	0.1662	2669	X-RAY DIFFRACTION	100
2.24-2.35	0.1805	111	0.1653	2703	X-RAY DIFFRACTION	100
2.35-2.47	0.1918	167	0.167	2651	X-RAY DIFFRACTION	100
2.47-2.62	0.1909	120	0.1708	2709	X-RAY DIFFRACTION	100
2.62-2.83	0.2101	148	0.1669	2683	X-RAY DIFFRACTION	100
2.83-3.11	0.1863	160	0.1683	2698	X-RAY DIFFRACTION	100
3.11-3.56	0.1628	146	0.1506	2727	X-RAY DIFFRACTION	100
3.56-4.47	0.1553	145	0.1494	2769	X-RAY DIFFRACTION	100
4.47-10	0.1954	144	0.1712	2913	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	1.5065	0.2247	1.2012	0.8893	-0.889	2.2608	-0.1203	0.1234	0.0009	0.0178	0.0425	-0.0412	-0.4608	0.3094	0.0351	0.2215	-0.0425	-0.0325	0.1115	0.021	0.1544	-36.7713	44.4234	11.2141
2	0.5178	-0.3175	-0.4354	2.1754	0.608	0.9424	-0.0813	-0.0753	-0.1252	0.1627	0.0257	-0.1206	0.1258	0.1036	0.058	0.2381	0.0238	-0.0445	0.1456	0.0526	0.1908	-29.472	16.6232	25.3886
3	3.4482	0.5421	0.9208	0.3017	-0.6322	3.0417	-0.0931	0.0593	-0.2638	-0.0439	0.0499	-0.071	0.1802	0.0406	0.116	0.2781	-0.0126	0.0065	0.0924	0.0016	0.1882	-36.418	11.6499	11.951
4	2.5587	0.3479	0.0823	2.157	-0.3133	1.3238	-0.1027	0.3249	-0.1468	-0.2268	0.0197	-0.0928	0.2295	0.0652	0.087	0.2372	-0.0105	0.0043	0.1224	0.0028	0.1433	-35.7154	14.9488	6.2455
5	6.8179	-2.9376	2.6636	4.1254	-2.1572	3.7343	0.0407	0.2977	-0.0343	-0.0667	-0.327	-0.5941	0.1636	0.4828	0.2499	0.2904	0.0477	0.013	0.1746	0.0569	0.3043	-19.8663	8.5275	11.8962
6	1.5275	0.6746	1.4152	1.6052	0.9362	2.7299	-0.1607	0.2214	0.0118	-0.1142	0.1865	-0.0596	0.0427	0.1884	-0.0425	0.2731	-0.0285	-0.0088	0.176	0.0381	0.2308	-37.3703	27.064	5.1286
7	1.179	0.207	-0.4558	1.7689	-0.0119	1.1651	-0.0093	-0.0158	-0.0027	0.2285	0.079	0.0233	0.0484	-0.0915	-0.0742	0.2261	-0.0047	-0.0185	0.109	0.0283	0.1504	-43.1877	34.2992	17.8875
8	5.1537	4.6491	-4.0441	4.2457	-3.7005	3.3865	0.3108	-0.1433	0.9573	0.54	0.0658	0.6718	-0.6837	-0.1095	-0.3701	0.3909	0.0407	0.0338	0.1679	0.0173	0.3149	-43.5513	50.871	21.1257
9	1.2956	0.1444	-0.1176	7.6157	-2.2968	3.6625	0.0009	-0.2618	0.0374	0.4858	0.1051	0.4544	-0.2608	-0.036	-0.1043	0.151	-0.0067	-0.0149	0.1787	0.0088	0.1425	-33.0056	37.9294	32.3409
10	1.3855	1.7532	0.453	4.2302	1.053	3.0613	0.041	-0.1007	-0.2022	0.2495	-0.0323	0.0582	0.4182	-0.3173	-0.0015	0.2283	-0.0234	0.0233	0.137	0.0323	0.1951	-53.7043	7.1383	21.5148
11	1.4413	-0.5089	-0.2386	1.71	1.1808	2.9157	-0.0768	0.0575	-0.0693	-0.1377	0.0886	0.1543	-0.0205	-0.1	-0.0035	0.2203	-0.0574	-0.0097	0.1267	0.0377	0.1789	-54.2725	16.1753	15.2738
12	2.8166	-0.2154	-1.3521	3.1714	-0.4547	5.9084	-0.0919	0.3404	-0.2202	-0.4614	0.205	-0.0642	0.8971	-0.0684	-0.0461	0.3101	-0.1022	-0.0321	0.1382	-0.0044	0.2129	-49.8264	8.0737	6.0643
13	2.8726	-0.7026	-0.9338	1.8688	-0.0886	0.7777	-0.0179	0.3929	-0.3874	-0.0026	-0.0265	0.1042	0.4903	-0.2964	0.0604	0.3785	-0.0694	-0.0375	0.1795	-0.0204	0.2254	-51.1433	6.8763	9.2074

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 92 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 93 through 115 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 116 through 171 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 172 through 204 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 27 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 28 through 82 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 83 through 100 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 101 through 125 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 126 through 147 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 148 through 190 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 191 through 207 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 208 through 228 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi