PDB-4ob2: Crystal Structure of Nitrile Hydratase from Pseudonocardia thermo...

ID or keywords:

Entry

Database: PDB / ID: 4ob2

Title

Crystal Structure of Nitrile Hydratase from Pseudonocardia thermophila bound to Butaneboronic Acid via Crystal Soaking

Components

(Cobalt-containing nitrile hydratase subunit ...) x 2

Keywords

LYASE / Nitrile Hydratase / nucleophile

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: 1.52 Å

Authors

Rui, W. / Salette, M. / Ruslan, S. / Richard, H. / Dali, L.

Citation

Journal: J.Am.Chem.Soc. / Year: 2014
Title: The active site sulfenic acid ligand in nitrile hydratases can function as a nucleophile.
Authors: Martinez, S. / Wu, R. / Sanishvili, R. / Liu, D. / Holz, R.

History

Deposition	Jan 6, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 26, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2019	Group: Database references / Derived calculations Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif Item: _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4ob2.cif.gz	198.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4ob2.ent.gz	166.3 KB	Display	PDB format
PDBx/mmJSON format	4ob2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4ob2_validation.pdf.gz	483.6 KB	Display	wwPDB validaton report
Full document	4ob2_full_validation.pdf.gz	489.2 KB	Display
Data in XML	4ob2_validation.xml.gz	25.2 KB	Display
Data in CIF	4ob2_validation.cif.gz	38.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ob/4ob2 ftp://data.pdbj.org/pub/pdb/validation_reports/ob/4ob2	HTTPS FTP

-
Related structure data

Related structure data	4ob0C 4ob1C 4ob3C C: citing same article (ref.)
Similar structure data	1ugs-d 3vyh-d 1ugq-d 1ugp-d 4ob0-d 4ob1-d 1ugr-d 4ob3-d 1ire-d 1sui-2 Search similar-shape structures by Omokage search (details) 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) #142 - Oct 2011 PDB Pioneers similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: Cobalt-containing nitrile hydratase subunit alpha

B: Cobalt-containing nitrile hydratase subunit beta

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	65.601, 65.601, 185.658
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	A-623- HOH
2	1	B-636- HOH
3	1	B-640- HOH
4	1	B-642- HOH

-
Cobalt-containing nitrile hydratase subunit ... , 2 types, 2 molecules AB

#1: Protein	Cobalt-containing nitrile hydratase subunit alpha / L-NHase / L-nitrilase Mass: 23901.277 Da / Num. of mol.: 1 / Fragment: Nitrile hydratase alpha subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SID2, nitrile hydratase
#2: Protein	Cobalt-containing nitrile hydratase subunit beta / L-NHase / L-nitrilase Mass: 26583.645 Da / Num. of mol.: 1 / Fragment: Nitrile hydratase beta subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SID3, nitrile hydratase

#1: Protein

Cobalt-containing nitrile hydratase subunit alpha / L-NHase / L-nitrilase

Mass: 23901.277 Da / Num. of mol.: 1 / Fragment: Nitrile hydratase alpha subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudonocardia thermophila (bacteria) / Production host:

Escherichia coli (E. coli) / References: UniProt: Q7SID2, nitrile hydratase

#2: Protein

Cobalt-containing nitrile hydratase subunit beta / L-NHase / L-nitrilase

Mass: 26583.645 Da / Num. of mol.: 1 / Fragment: Nitrile hydratase beta subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudonocardia thermophila (bacteria) / Production host:

Escherichia coli (E. coli) / References: UniProt: Q7SID3, nitrile hydratase

-
Non-polymers , 5 types, 584 molecules

#3: Chemical	ChemComp-BUB / 1-BUTANE BORONIC ACID Mass: 101.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₁BO₂
#4: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	... ChemComp-MOH / METHANOL Mass: 32.042 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: CH₄O
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.15 %
Crystal grow	Temperature: 276 K / Method: evaporation / pH: 7.5 Details: 1.4 M sodium citrate tribasic, 0.1 M HEPES, 20 mM Phenyl Boronic Acid, pH 7.5, EVAPORATION, temperature 276K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 1 Å

Detector

Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2012

Radiation

Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.52→50 Å / Num. all: 325277 / Num. obs: 72603 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / R_merge(I) obs: 0.054 / Net I/σ(I): 16.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Diffraction-ID	% possible all
1.52-1.55	4.4	0.824	1.5	3539	1	99.2
1.55-1.57	4.4	0.718	1.8	3567	1	99.3
1.57-1.6	4.4	0.621	2.2	3605	1	99.3

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASES		phasing
PHENIX	(phenix.refine: 1.8.3_1479)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.52→35.944 Å / SU ML: 0.12 / σ(F): 1.36 / Phase error: 18.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1828	3236	5.06 %	Random
R_work	0.1518	-	-	-
obs	0.1534	63933	87.91 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.52→35.944 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3458	0	104	550	4112

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	3711
X-RAY DIFFRACTION	f_angle_d	1.142	4998
X-RAY DIFFRACTION	f_dihedral_angle_d	14.311	1403
X-RAY DIFFRACTION	f_chiral_restr	0.049	513
X-RAY DIFFRACTION	f_plane_restr	0.006	654

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 (%)
1.5172-1.5399	0.1911	9	0.2051	315	X-RAY DIFFRACTION	10
1.5399-1.564	0.2479	29	0.1979	613	X-RAY DIFFRACTION	21
1.564-1.5896	0.2489	44	0.1954	1179	X-RAY DIFFRACTION	39
1.5896-1.617	0.2458	107	0.1983	1989	X-RAY DIFFRACTION	68
1.617-1.6464	0.2386	146	0.193	2682	X-RAY DIFFRACTION	89
1.6464-1.6781	0.2387	155	0.1899	2816	X-RAY DIFFRACTION	95
1.6781-1.7123	0.1955	155	0.1847	2902	X-RAY DIFFRACTION	98
1.7123-1.7496	0.206	158	0.1747	2913	X-RAY DIFFRACTION	99
1.7496-1.7903	0.2346	172	0.1691	2960	X-RAY DIFFRACTION	99
1.7903-1.835	0.2043	165	0.1648	2943	X-RAY DIFFRACTION	100
1.835-1.8846	0.2008	160	0.1609	2964	X-RAY DIFFRACTION	100
1.8846-1.9401	0.1848	143	0.1648	3018	X-RAY DIFFRACTION	100
1.9401-2.0027	0.1873	144	0.1591	2988	X-RAY DIFFRACTION	100
2.0027-2.0743	0.1838	176	0.1484	2968	X-RAY DIFFRACTION	100
2.0743-2.1573	0.209	133	0.1533	3003	X-RAY DIFFRACTION	100
2.1573-2.2555	0.1858	173	0.149	2985	X-RAY DIFFRACTION	100
2.2555-2.3744	0.166	175	0.1484	2998	X-RAY DIFFRACTION	100
2.3744-2.5231	0.1903	164	0.1537	3041	X-RAY DIFFRACTION	100
2.5231-2.7179	0.1756	164	0.1558	2996	X-RAY DIFFRACTION	100
2.7179-2.9912	0.1946	177	0.1571	3058	X-RAY DIFFRACTION	100
2.9912-3.4238	0.168	161	0.1399	3025	X-RAY DIFFRACTION	100
3.4238-4.3125	0.1422	163	0.1219	3097	X-RAY DIFFRACTION	100
4.3125-35.954	0.176	163	0.1483	3244	X-RAY DIFFRACTION	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	0.6935	0.2789	0.8426	0.4249	0.4801	7.1685	-0.0678	0.0923	0.0564	-0.0367	0.0609	-0.0336	-0.1902	0.3565	-0.0265	0.1382	-0.0156	-0.0213	0.1018	0.0137	0.1582	-5.3697	-15.437	196.7627
2	0.3774	-1.2181	-0.6024	4.7712	2.0814	0.9577	-0.0773	-0.0563	0.0073	0.1797	0.1429	-0.2308	0.0517	0.1371	-0.098	0.1578	0.0103	-0.0437	0.1442	0.0078	0.1477	4.2724	-35.9282	210.2416
3	1.0457	-0.2486	0.2212	0.9969	-0.1261	0.6958	-0.0102	0.0816	-0.053	-0.0136	-0.0177	-0.058	0.1112	0.0806	0.0154	0.1274	0.0165	0.011	0.088	-0.0102	0.1019	-1.8715	-48.1207	197.0536
4	5.0219	-1.8062	1.816	2.9653	-1.5818	3.255	-0.1133	0.1258	0.3641	0.1377	-0.1436	-0.414	-0.0674	0.2322	0.2728	0.1657	0.0171	-0.0072	0.127	0.0231	0.1867	10.409	-48.137	196.7365
5	0.3798	0.2107	0.4927	0.2176	0.3823	0.9265	-0.0428	0.1146	0.1409	-0.0292	0.0449	-0.0387	-0.045	0.1624	0.0007	0.1584	-0.024	0.0025	0.1471	0.012	0.1398	-5.1249	-32.6521	190.6244
6	2.7778	0.4361	-3.0579	1.8067	-1.5437	5.3202	0.0352	-0.1424	-0.0693	0.134	-0.0556	-0.1444	0.0222	0.0269	0.0153	0.1517	-0.007	-0.0454	0.1053	0.0023	0.1345	-4.7908	-25.0775	208.9627
7	0.5807	0.3864	0.0842	0.3744	-0.0526	0.6366	0.0026	-0.002	0.0393	0.0258	0.008	0.0444	-0.0516	-0.0234	-0.0043	0.1395	0.0058	-0.0068	0.091	0.0029	0.1286	-14.1382	-26.0291	201.4886
8	5.6576	2.4082	-2.1571	2.3105	-0.9501	2.2181	-0.0019	0.013	0.5967	0.0332	0.0299	0.2833	-0.2658	-0.0793	-0.0597	0.212	0.0327	-0.0235	0.1274	-0.0067	0.2118	-12.4023	-9.3522	206.4648
9	1.0102	0.0362	-0.0293	5.2912	-3.363	3.341	-0.0613	-0.0496	0.1246	0.3195	-0.0234	-0.1812	-0.4107	0.0673	0.0762	0.1496	-0.0199	-0.0138	0.1346	-0.0217	0.1601	-0.4956	-11.444	215.1665
10	1.12	0.4634	0.7914	2.9659	3.2527	3.7099	0.0873	-0.2288	-0.1701	0.7958	-0.0337	-0.1013	0.5234	0.0031	-0.0333	0.2443	-0.0045	-0.0318	0.1552	0.0267	0.1585	-2.5068	-32.2301	220.2549
11	1.1069	0.964	0.2022	2.0402	0.6952	1.3211	0.0405	-0.1436	-0.1575	0.215	-0.0325	0.0263	0.2581	-0.0874	0.0168	0.1559	0.0144	0.0338	0.0953	0.0204	0.1454	-22.1565	-52.332	206.2631
12	0.7708	-0.2706	0.068	0.9741	0.4221	1.9472	-0.0194	-0.0043	0.0099	-0.0141	0.0274	0.0495	-0.0044	-0.0136	-0.023	0.1038	-0.0135	0.0166	0.0839	0.0056	0.1123	-22.5332	-43.5327	200.9639
13	1.9943	-0.2762	-1.1226	1.7003	-0.6472	6.1326	-0.0834	0.1792	-0.1193	-0.1595	-0.0073	0.0171	0.3582	0.0919	0.1088	0.1202	-0.0212	0.0072	0.0597	-0.0136	0.1146	-18.3102	-51.783	191.9037
14	2.112	-0.9549	-1.0866	0.9768	0.4555	2.0593	-0.0062	0.2488	-0.2779	-0.0328	-0.0686	0.0661	0.3274	-0.0509	0.0274	0.1663	0.0049	0.0051	0.0986	-0.0269	0.1222	-19.0481	-52.7947	194.2427

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 182 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 183 through 204 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 27 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 28 through 42 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 43 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 112 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 113 through 125 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 126 through 147 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 148 through 190 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 191 through 207 )
14	X-RAY DIFFRACTION	14	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

-
Cobalt-containing nitrile hydratase subunit ... , 2 types, 2 molecules AB

-
Non-polymers , 5 types, 584 molecules

-
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

-Cobalt-containing nitrile hydratase subunit ... , 2 types, 2 molecules AB

-Non-polymers , 5 types, 584 molecules

-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

-
Cobalt-containing nitrile hydratase subunit ... , 2 types, 2 molecules AB

-
Non-polymers , 5 types, 584 molecules

-
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