PDB-4ob1: Crystal Structure of Nitrile Hydratase from Pseudonocardia thermo...

ID or keywords:

Entry

Database: PDB / ID: 4ob1

Title

Crystal Structure of Nitrile Hydratase from Pseudonocardia thermophila bound to Butaneboronic Acid via Co-crystallization

Components

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

Keywords

HYDROLASE / Nitrile Hydratase / Nulceophile

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: 1.631 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
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ob1.cif.gz	208.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4ob1.ent.gz	163.6 KB	Display	PDB format
PDBx/mmJSON format	4ob1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4ob1_validation.pdf.gz	464.7 KB	Display	wwPDB validaton report
Full document	4ob1_full_validation.pdf.gz	471.1 KB	Display
Data in XML	4ob1_validation.xml.gz	26.8 KB	Display
Data in CIF	4ob1_validation.cif.gz	42.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ob/4ob1 ftp://data.pdbj.org/pub/pdb/validation_reports/ob/4ob1	HTTPS FTP

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Related structure data

Related structure data	4ob0C 4ob2C 4ob3C C: citing same article (ref.)
Similar structure data	1ire-d 1ugr-d 1ugs-d 1ugq-d 4ob3-d 1ugp-d 6bzz-2 4ob0-d 2c8n-5 3vyh-d Search similar-shape structures by Omokage search (details) 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) #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

59.8 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)	65.870, 65.870, 186.150
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-638- HOH
2	1	B-635- HOH
3	1	B-641- HOH
4	1	B-644- HOH
5	1	B-665- HOH
6	1	B-721- HOH

#1: Protein	Cobalt-containing nitrile hydratase subunit alpha / L-NHase / L-nitrilase Mass: 33060.879 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
#3: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical	ChemComp-BUB / 1-BUTANE BORONIC ACID Mass: 101.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₁BO₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 748 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.95 Å³/Da / Density % sol: 37.07 %
Crystal grow	Temperature: 276 K / Method: evaporation / pH: 7.5 Details: 1.4 M sodium citrate tribasic, 0.1 M HEPES, 20 mM Butaneboronic Acid, pH 7.5, EVAPORATION, temperature 276K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2012
Radiation	Monochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.63→36.06 Å / Num. all: 390048 / Num. obs: 59389 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / R_merge(I) obs: 0.06
Reflection shell	Resolution: 1.63→1.72 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.207 / Mean I/σ(I) obs: 7.6 / Num. unique all: 8533 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.631→36.06 Å / SU ML: 0.12 / σ(F): 1.36 / Phase error: 13.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1658	2998	5.05 %	Random
R_work	0.1421	-	-	-
obs	0.1433	59344	99.95 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.631→36.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3461	0	8	748	4217

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.019	3687
X-RAY DIFFRACTION	f_angle_d	1.829	5028
X-RAY DIFFRACTION	f_dihedral_angle_d	13.923	1415
X-RAY DIFFRACTION	f_chiral_restr	0.087	527
X-RAY DIFFRACTION	f_plane_restr	0.01	663

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 (%)
1.631-1.6578	0.17	163	0.1384	2623	X-RAY DIFFRACTION	100
1.6578-1.6863	0.2071	157	0.1501	2639	X-RAY DIFFRACTION	100
1.6863-1.717	0.1984	145	0.1463	2582	X-RAY DIFFRACTION	100
1.717-1.75	0.1663	135	0.1446	2667	X-RAY DIFFRACTION	100
1.75-1.7858	0.1991	168	0.1394	2652	X-RAY DIFFRACTION	100
1.7858-1.8246	0.1893	150	0.1359	2605	X-RAY DIFFRACTION	100
1.8246-1.867	0.175	129	0.1364	2659	X-RAY DIFFRACTION	100
1.867-1.9137	0.1856	134	0.1311	2680	X-RAY DIFFRACTION	100
1.9137-1.9654	0.1618	137	0.1345	2655	X-RAY DIFFRACTION	100
1.9654-2.0233	0.153	122	0.1371	2673	X-RAY DIFFRACTION	100
2.0233-2.0886	0.1837	134	0.1312	2655	X-RAY DIFFRACTION	100
2.0886-2.1632	0.1671	128	0.1407	2691	X-RAY DIFFRACTION	100
2.1632-2.2498	0.1824	136	0.145	2696	X-RAY DIFFRACTION	100
2.2498-2.3522	0.155	147	0.1407	2690	X-RAY DIFFRACTION	100
2.3522-2.4762	0.1702	126	0.1443	2678	X-RAY DIFFRACTION	100
2.4762-2.6313	0.1619	176	0.1489	2668	X-RAY DIFFRACTION	100
2.6313-2.8344	0.1695	136	0.1524	2694	X-RAY DIFFRACTION	100
2.8344-3.1194	0.1819	138	0.1543	2727	X-RAY DIFFRACTION	100
3.1194-3.5705	0.1572	126	0.1372	2746	X-RAY DIFFRACTION	100
3.5705-4.4971	0.1242	159	0.1279	2745	X-RAY DIFFRACTION	100
4.4971-36.0687	0.1719	152	0.1567	2921	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	0.5933	0.174	-0.3173	0.0828	0.2921	5.5224	-0.0294	0.0665	-0.0629	-0.0168	0.028	0.0072	0.114	-0.2899	-0.0516	0.0818	-0.0126	0.0218	0.054	-0.0153	0.0879	5.1067	15.5546	10.8149
2	0.183	-0.7198	0.379	3.3687	-1.4745	0.7634	-0.0459	-0.0289	-0.0198	0.1523	0.1249	0.2557	-0.0816	-0.1431	-0.0827	0.0934	0.0207	0.0372	0.1007	-0.0059	0.0881	-4.0155	35.4712	24.7164
3	4.0648	-0.543	-0.6831	1.5107	0.4607	1.988	-0.1155	-0.1557	0.3203	0.3514	0.0584	-0.1163	-0.1097	0.0828	0.0079	0.2148	0.0588	-0.0164	0.0969	-0.0163	0.1142	-1.5542	56.7337	24.4896
4	1.0488	-0.2517	-0.0569	1.0361	-0.1085	0.5476	0.0053	0.1032	0.0508	-0.0219	-0.0248	0.0267	-0.1159	-0.0357	0.0173	0.0891	0.0206	-0.0042	0.0625	0.0052	0.0594	4.2011	45.8208	8.6662
5	3.9683	-2.6961	-1.2325	3.0722	1.3777	1.2371	-0.0087	0.213	-0.1562	0.0363	-0.1599	0.35	-0.0705	-0.1928	0.1325	0.1281	0.0401	0.0032	0.1012	-0.0125	0.1311	-11.6913	51.441	11.2174
6	1.7643	0.6095	-1.4438	0.3757	-0.5707	1.218	-0.0604	0.1412	-0.15	-0.0839	0.0524	0.015	0.0379	-0.1861	-0.0051	0.1069	-0.0141	-0.0123	0.0923	-0.0221	0.0779	5.6702	32.8396	4.8259
7	3.1619	0.3691	4.1194	1.5628	1.6637	6.4909	0.0468	-0.0653	0.0288	0.0811	-0.0236	0.0379	-0.0045	0.0225	0.0079	0.0865	-0.0081	0.0318	0.0741	-0.0005	0.0674	4.8825	25.2658	23.3664
8	0.8288	0.5571	-0.0065	0.5903	0.1103	1.0184	-0.012	-0.0103	-0.0644	0.022	0.0062	-0.0631	0.0538	0.059	0.0012	0.0784	0.0112	0.0047	0.0448	0.0015	0.0771	14.3993	26.1001	16.0875
9	4.7687	1.3166	2.2274	1.5124	1.0652	2.7999	0.0087	-0.0644	-0.412	0.0241	0.041	-0.2213	0.2935	0.0724	-0.0728	0.1478	0.0449	0.0226	0.0731	0.0011	0.1503	11.981	8.7793	20.5746
10	0.2474	0.1434	0.3555	4.1846	3.0968	2.6642	-0.0199	-0.044	-0.0973	0.2836	-0.0146	0.1196	0.334	-0.0515	0.0086	0.1356	-0.0255	0.0166	0.1072	0.0186	0.1286	0.5802	11.3143	29.8417
11	1.7478	0.28	-0.4839	3.6516	-3.5149	3.8713	0.0777	-0.1711	0.1001	0.5111	-0.1591	-0.013	-0.3701	0.0219	0.0552	0.1604	0.0024	0.0223	0.0992	-0.0187	0.0758	2.3904	32.2831	34.3504
12	0.8948	0.9097	-0.272	1.6558	-0.6046	1.1125	0.039	-0.1226	0.151	0.2168	-0.0053	-0.0374	-0.2349	0.0375	-0.002	0.1161	0.0182	-0.0256	0.0658	-0.0246	0.1116	21.9529	52.2904	21.193
13	0.8873	-0.3862	0.1302	1.0663	-0.4435	1.7714	-0.0019	0.0382	0.0484	-0.0398	0.0101	-0.0394	-0.0803	-0.0529	-0.0127	0.0597	-0.0082	-0.0126	0.034	-0.0035	0.057	20.3905	47.2635	10.8971
14	2.1783	-0.126	1.4884	1.7813	0.6962	1.3605	-0.1314	0.1519	0.1282	0.0241	0.0524	-0.1921	-0.232	0.1326	-0.0859	0.0906	-0.019	-0.0078	0.0386	0.0114	0.0661	21.907	51.3676	12.1354

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 63 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 83 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 84 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 42 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 43 through 83 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 84 through 100 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 101 through 112 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 113 through 125 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 126 through 147 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 148 through 212 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 213 through 228 )

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