PDB-5j8d: Structure of nitroreductase from E. cloacae complexed with nicoti...

ID or keywords:

Entry

Database: PDB / ID: 5j8d

Title

Structure of nitroreductase from E. cloacae complexed with nicotinic acid adenine dinucleotide

Components

Oxygen-insensitive NAD(P)H nitroreductase

Keywords

OXIDOREDUCTASE / Nitroreductase / Complex / NAAD / Substrate

Function / homology

Function and homology information

oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 2,4,6-trinitrotoluene catabolic process / Oxidoreductases / cytosol
Similarity search - Function

Biological species

Enterobacter cloacae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Haynes, C.A. / Koder, R.L. / Miller, A.F. / Rodgers, D.W.

Funding support

United States, 4items

Organization	Grant number	Country
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	NS38401	United States
National Science Foundation (NSF, United States)	MCB 9904886	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM110787	United States
National Science Foundation (NSF, United States)	IIA-1355438	United States

Citation

Journal: Structure / Year: 2017
Title: Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase.
Authors: Pitsawong, W. / Haynes, C.A. / Koder, R.L. / Rodgers, D.W. / Miller, A.F.

History

Deposition	Apr 7, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 17, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Dec 6, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5j8d.cif.gz	371.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5j8d.ent.gz	305.2 KB	Display	PDB format
PDBx/mmJSON format	5j8d.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5j8d_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	5j8d_full_validation.pdf.gz	2.8 MB	Display
Data in XML	5j8d_validation.xml.gz	44.6 KB	Display
Data in CIF	5j8d_validation.cif.gz	65.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j8/5j8d ftp://data.pdbj.org/pub/pdb/validation_reports/j8/5j8d	HTTPS FTP

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Related structure data

Related structure data	5j8gC 1kqcS 1kqb 1kqd S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1nec-2 1oo6-d 2wbe-1 1kqc-1 3tjl-d 1v5y-d 1icu-2 1ylr-d 5kt1-d 6u31-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Oxygen-insensitive NAD(P)H nitroreductase

B: Oxygen-insensitive NAD(P)H nitroreductase

C: Oxygen-insensitive NAD(P)H nitroreductase

D: Oxygen-insensitive NAD(P)H nitroreductase

hetero molecules

99.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Oxygen-insensitive NAD(P)H nitroreductase

B: Oxygen-insensitive NAD(P)H nitroreductase

hetero molecules

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

2

C: Oxygen-insensitive NAD(P)H nitroreductase

D: Oxygen-insensitive NAD(P)H nitroreductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.380, 113.140, 80.700
Angle α, β, γ (deg.)	90.000, 92.590, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Oxygen-insensitive NAD(P)H nitroreductase / NR Mass: 23850.980 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: nfsB, nfnB, nfsI / Plasmid: PET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01234, Oxidoreductases
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+ Mass: 665.418 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₆O₁₅P₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1024 / 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: 2.36 Å³/Da / Density % sol: 47.89 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 100 mM homopipes (pH 4.8), 50 mM sodium acetate and 15% w/v polyethylene glycol 4000. Protein at 4.75 mg/ml initial concentration in 10 mM HEPES (pH 7.0) and 50 mM KCl.

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Data collection

Diffraction	Mean temperature: 115 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
Detector	Type: CUSTOM-MADE / Detector: CCD / Date: Jan 3, 2003 / Details: Mirrors
Radiation	Monochromator: Double crystal silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.85→19.842 Å / B_iso Wilson estimate: 12.38 Å²

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Processing

Software

Name	Version	Classification
PHENIX		refinement
PDB_EXTRACT	3.2	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
CNS		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1KQC

1kqc

Resolution: 1.85→19.842 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 21.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2124	6488	9.12 %	Random selection
R_work	0.1747	64652	-	-
obs	0.178	71140	94.43 %	-

Solvent computation

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

Displacement parameters

B_iso max: 102.71 Å² / B_iso mean: 21.3138 Å² / B_iso min: 3.24 Å²

Refinement step

Cycle: final / Resolution: 1.85→19.842 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6708	0	300	1024	8032
B_iso mean	-	-	23.43	29.21	-
Num. residues	-	-	-	-	864

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7168
X-RAY DIFFRACTION	f_angle_d	0.653	9756
X-RAY DIFFRACTION	f_chiral_restr	0.04	1088
X-RAY DIFFRACTION	f_plane_restr	0.005	1396
X-RAY DIFFRACTION	f_dihedral_angle_d	11.356	4352

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.85-1.871	0.2852	166	0.2351	1689	1855	75
1.871-1.893	0.3008	187	0.2112	1862	2049	80
1.893-1.9161	0.2815	214	0.214	1848	2062	84
1.9161-1.9403	0.2438	185	0.1968	1969	2154	87
1.9403-1.9658	0.2409	185	0.1896	2049	2234	88
1.9658-1.9927	0.2325	197	0.1901	2023	2220	90
1.9927-2.0212	0.234	208	0.1857	2085	2293	91
2.0212-2.0513	0.2166	209	0.182	2107	2316	92
2.0513-2.0833	0.2279	215	0.1819	2097	2312	94
2.0833-2.1174	0.2185	220	0.1782	2144	2364	94
2.1174-2.1539	0.2299	214	0.1767	2185	2399	95
2.1539-2.193	0.229	214	0.1777	2159	2373	96
2.193-2.2351	0.2273	219	0.1741	2194	2413	96
2.2351-2.2807	0.2101	221	0.1766	2201	2422	96
2.2807-2.3302	0.2136	241	0.1729	2201	2442	97
2.3302-2.3843	0.2363	211	0.1783	2180	2391	96
2.3843-2.4439	0.2177	235	0.1737	2235	2470	97
2.4439-2.5098	0.2194	248	0.1815	2200	2448	98
2.5098-2.5835	0.2179	203	0.1667	2239	2442	98
2.5835-2.6667	0.1988	218	0.1739	2221	2439	98
2.6667-2.7618	0.2086	228	0.1677	2256	2484	98
2.7618-2.8721	0.2115	237	0.1764	2241	2478	98
2.8721-3.0023	0.1895	222	0.1701	2240	2462	99
3.0023-3.16	0.2023	227	0.1688	2251	2478	99
3.16-3.3571	0.1953	210	0.1699	2306	2516	99
3.3571-3.6149	0.1887	234	0.1607	2270	2504	100
3.6149-3.9761	0.1959	223	0.1673	2289	2512	100
3.9761-4.5454	0.2048	240	0.1553	2288	2528	100
4.5454-5.704	0.1798	225	0.1675	2307	2532	100
5.704-19.8432	0.2061	232	0.1841	2316	2548	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	0.0348	-0.0712	-0.0442	0.9585	0.4722	0.708	-0.0697	0.0132	0.077	0.0641	0.0472	-0.2536	-0.1456	0.1427	0.0217	0.2054	-0.0271	-0.1012	0.1081	0.0076	0.1796	50.5277	114.4649	31.6367
2	0.8372	0.4485	0.3901	1.8922	0.7694	1.6773	-0.0999	0.0598	0.1275	0.163	0.0191	-0.0757	-0.1247	0.0663	0.0475	0.1419	0.006	-0.0689	0.0936	0.0229	0.099	41.3479	114.1421	24.558
3	7.9632	-5.2546	-6.6252	4.6717	4.6536	7.0173	-0.1659	0.2933	-0.6178	0.1229	-0.1434	0.4245	0.4266	-0.1796	0.3142	0.2506	-0.0354	-0.0418	0.1613	0.0078	0.1771	34.6122	92.4364	19.9474
4	0.4369	0.2065	0.1422	0.9132	0.2506	0.8255	-0.0827	-0.0263	0.0873	0.1404	0.0417	-0.1065	-0.1099	-0.0455	0.0453	0.2239	0.0092	-0.0918	0.0687	-0.0095	0.1287	41.5869	113.686	36.2721
5	0.2459	-0.1395	0.1342	0.6082	-0.1306	0.5436	0.0249	0.0206	-0.0843	0.1054	0.0262	-0.0284	0.2517	0.0098	-0.0518	0.3322	0.0161	-0.1411	0.0721	0.0056	0.1527	46.1841	93.5896	40.9447
6	5.1566	1.5127	-0.1684	0.6145	-0.3487	4.6175	0.149	-0.4086	0.5005	0.4641	-0.088	0.0781	-0.2458	-0.1924	-0.0986	0.2963	0.0642	-0.0474	0.1081	-0.0448	0.2092	37.128	113.8295	56.6816
7	4.2399	1.4039	3.2197	2.8676	1.9933	6.2061	-0.1419	0.1363	0.7078	-0.1997	-0.0014	0.8945	-0.869	-0.7857	-0.124	0.6944	0.231	0.0274	0.8714	0.1892	0.6296	28.2875	117.052	47.0486
8	0.587	0.0978	0.4579	0.9146	0.0645	1.6449	0.0566	0.017	-0.0473	0.1269	0.0196	-0.0524	0.194	-0.0035	-0.0499	0.2337	-0.0106	-0.1187	0.0722	-0.0012	0.1141	43.2362	97.491	34.6004
9	1.0443	-0.1162	0.8482	2.203	-0.789	0.9229	0.0105	0.1895	0.1373	-0.0422	-0.1828	-0.267	-0.0643	0.1414	0.1667	0.1057	-0.0399	0.0307	0.1437	0.0247	0.0711	34.7888	52.0132	-4.3126
10	0.9534	2.049	-0.6966	6.3628	-4.249	5.1365	0.005	0.1414	-0.004	-0.1226	0.0391	0.0223	0.001	-0.0346	-0.0105	0.0455	0.0044	0.0126	0.0526	0.0076	0.076	20.2813	48.0368	-8.6071
11	0.8289	0.5616	0.1838	2.2826	-0.1311	0.8078	-0.0397	-0.0928	0.1763	0.159	-0.0494	0.0619	-0.1445	-0.0426	0.0551	0.0745	0.002	0.0127	0.0809	-0.0147	0.0963	19.862	54.2951	4.8817
12	2.7673	-0.1108	-0.1435	0.641	0.1812	4.5461	0.0882	0.0708	-0.1707	0.0322	0.0843	0.0797	0.193	-0.3369	0.2039	0.0518	-0.0226	0.0522	0.0864	0.0084	0.234	5.1627	32.8319	0.9718
13	3.6305	2.8121	4.5676	4.0073	4.6438	7.6929	0.3265	-0.4174	-0.2448	0.4296	-0.0746	0.1734	0.4128	-0.5971	-0.2263	0.1872	-0.0171	0.0582	0.2896	0.0859	0.2907	8.9712	29.6731	13.2835
14	1.0667	0.1245	-0.0631	1.9064	0.1711	1.2481	0.0151	-0.0842	0.0658	0.1499	-0.052	0.1231	0.0186	-0.0561	0.0163	0.0412	-0.0108	-0.0024	0.06	-0.0037	0.0428	22.9197	48.7335	7.0123
15	1.9553	2.0752	-0.2471	3.9751	-1.7457	5.3475	0.0782	-0.1966	0.3345	0.2923	-0.067	0.6201	-0.1591	-0.4763	0.0425	0.1475	-0.0095	-0.0008	0.0682	-0.0677	0.1513	15.8325	53.7456	8.1679
16	1.3976	-0.8517	1.04	2.8598	-2.1319	2.0508	-0.0392	0.1536	0.143	0.2279	-0.2566	-0.4978	-0.1953	0.2157	0.3083	0.097	-0.0435	-0.009	0.1607	0.0161	0.1147	41.8645	46.3482	5.1297
17	0.8765	0.1803	0.3361	1.4982	-0.0572	0.6439	-0.0051	0.0978	-0.0659	-0.0575	0.0036	-0.1841	-0.0466	0.0944	0.0036	0.0528	-0.0073	0.0286	0.0952	0.0062	0.0711	33.5427	31.9128	1.9424
18	3.7869	1.034	0.5387	5.3341	0.4981	5.2943	0.2932	-0.2866	-0.2643	0.1757	-0.0727	0.1756	0.4994	-0.1812	-0.1712	0.2004	-0.0418	-0.0356	0.0741	0.0352	0.1217	26.055	17.8917	11.1919
19	0.8669	0.1221	-0.0784	0.4023	0.2639	0.2736	-0.0361	0.0153	0.1596	0.1299	-0.0229	-0.1124	-0.2156	0.2501	-0.0035	0.2554	-0.1041	-0.0816	0.1567	0.0527	0.1345	41.2638	42.4832	15.0444
20	7.0964	3.3405	-4.3957	3.9933	-1.8907	4.6903	0.2579	-0.4875	0.5561	0.7084	-0.1521	-0.1403	-0.4887	0.6033	-0.0833	0.4088	-0.0121	-0.1401	0.2334	-0.0022	0.2454	35.5208	54.076	21.4062
21	0.8719	-0.0618	0.2861	1.7726	0.1065	1.0729	0.0255	-0.0618	-0.0542	0.1883	0.0053	-0.106	0.0988	0.0153	-0.0264	0.0567	-0.0199	0.0067	0.0644	0.0088	0.0663	28.1001	30.4571	9.8834
22	2.5484	-1.3105	0.0157	8.4709	1.893	2.1524	-0.0603	0.1323	0.0252	-0.0425	0.0036	0.4231	-0.1408	-0.0434	0.0775	0.0369	-0.0105	0.0031	0.0955	0.012	0.0646	12.0227	42.4153	-3.7179

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 53 )	A	2 - 53
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 54 through 110 )	A	54 - 110
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 111 through 134 )	A	111 - 134
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 135 through 217 )	A	135 - 217
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 91 )	B	2 - 91
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 92 through 110 )	B	92 - 110
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 111 through 134 )	B	111 - 134
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 135 through 217 )	B	135 - 217
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 2 through 23 )	C	2 - 23
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 24 through 35 )	C	24 - 35
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 36 through 91 )	C	36 - 91
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 92 through 110 )	C	92 - 110
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 111 through 134 )	C	111 - 134
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 135 through 175 )	C	135 - 175
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 176 through 192 )	C	176 - 192
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 193 through 217 )	C	193 - 217
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 2 through 53 )	D	2 - 53
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 54 through 77 )	D	54 - 77
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 78 through 110 )	D	78 - 110
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 111 through 134 )	D	111 - 134
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 135 through 201 )	D	135 - 201
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 202 through 217 )	D	202 - 217

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-Yorodumi

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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

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Yorodumi