PDB-5j8g: Structure of nitroreductase from E. cloacae complexed with para-n...

ID or keywords:

Entry

Database: PDB / ID: 5j8g

Title

Structure of nitroreductase from E. cloacae complexed with para-nitrobenzoic acid

Components

Oxygen-insensitive NAD(P)H nitroreductase

Keywords

OXIDOREDUCTASE / Nitroreductase / Complex / pNBA / 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: 1.9 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	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	5j8g_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	5j8g_full_validation.pdf.gz	1.7 MB	Display
Data in XML	5j8g_validation.xml.gz	41.1 KB	Display
Data in CIF	5j8g_validation.cif.gz	59 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j8/5j8g ftp://data.pdbj.org/pub/pdb/validation_reports/j8/5j8g	HTTPS FTP

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Related structure data

Related structure data	5j8dC 1kqb 1kqc 1kqd C: citing same article (ref.)
Similar structure data	1oon-d 1oo6-d 1yki-1 1kqd-2 1ylu-d 1kqb-1 3x21-2 1idt-d 1icv-1 1kqd-1 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

97.9 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
48.9 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
48.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.410, 113.440, 82.290
Angle α, β, γ (deg.)	90.000, 101.550, 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-4NB / 4-NITROBENZOIC ACID / PARA NITROBENZOIC ACID Mass: 167.119 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₇H₅NO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 790 / 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: 2.51 Å³/Da / Density % sol: 51.04 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 100 mM homopipes (pH 4.8), 20 mM para-nitrobenzoic acid, and 13% 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: 14-ID-B / Wavelength: 0.9 Å

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2002 / Details: Mirrors

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9 Å / Relative weight: 1

Reflection

Resolution: 1.9→19.923 Å / B_iso Wilson estimate: 20.01 Å²

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.9-1.97	3.2	0.27	7234	0.885	0.176	0.323	1.058	97.6
1.97-2.05	3.3	0.233	7272	0.924	0.152	0.279	1.08	97.8
2.05-2.14	3.3	0.184	7245	0.943	0.121	0.221	1.175	97.7
2.14-2.25	3.3	0.161	7302	0.953	0.105	0.193	1.18	98.2
2.25-2.39	3.3	0.139	7337	0.961	0.091	0.167	1.196	98.2
2.39-2.58	3.3	0.119	7292	0.97	0.078	0.143	1.082	98.4
2.58-2.84	3.3	0.102	7348	0.978	0.066	0.122	1.108	98.7
2.84-3.25	3.3	0.085	7386	0.985	0.056	0.102	0.994	99
3.25-4.08	3.2	0.074	7390	0.987	0.048	0.089	1.076	98.9
4.08-20	3.2	0.064	7444	0.99	0.042	0.077	1.058	98.4

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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 / Resolution: 1.9→19.923 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1972	7369	10.12 %
R_work	0.1664	65425	-
obs	0.1696	72794	98.29 %

Solvent computation

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

Displacement parameters

B_iso max: 143.22 Å² / B_iso mean: 28.6758 Å² / B_iso min: 7.48 Å²

Refinement step

Cycle: final / Resolution: 1.9→19.923 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6708	0	172	790	7670
B_iso mean	-	-	18.91	37.46	-
Num. residues	-	-	-	-	864

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7024
X-RAY DIFFRACTION	f_angle_d	0.538	9528
X-RAY DIFFRACTION	f_chiral_restr	0.039	1056
X-RAY DIFFRACTION	f_plane_restr	0.004	1344
X-RAY DIFFRACTION	f_dihedral_angle_d	10.036	4236

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 (%)
1.9-1.9216	0.2627	259	0.1986	2198	2457	97
1.9216-1.9442	0.2184	242	0.1792	2138	2380	98
1.9442-1.9679	0.202	235	0.1765	2147	2382	98
1.9679-1.9928	0.2032	231	0.1764	2157	2388	98
1.9928-2.019	0.1923	232	0.1677	2217	2449	98
2.019-2.0466	0.2097	237	0.1695	2116	2353	98
2.0466-2.0758	0.2004	212	0.1705	2210	2422	98
2.0758-2.1067	0.218	234	0.1713	2186	2420	98
2.1067-2.1396	0.206	241	0.1657	2148	2389	98
2.1396-2.1747	0.2096	242	0.167	2205	2447	98
2.1747-2.2121	0.2055	239	0.1686	2139	2378	98
2.2121-2.2523	0.1939	245	0.1581	2182	2427	98
2.2523-2.2956	0.2151	253	0.1707	2150	2403	98
2.2956-2.3423	0.21	239	0.1709	2198	2437	98
2.3423-2.3932	0.2029	256	0.1656	2173	2429	98
2.3932-2.4488	0.2049	241	0.1694	2150	2391	98
2.4488-2.5099	0.1969	228	0.1685	2229	2457	98
2.5099-2.5776	0.2112	245	0.1673	2161	2406	99
2.5776-2.6533	0.2075	252	0.1631	2193	2445	99
2.6533-2.7387	0.208	259	0.17	2166	2425	99
2.7387-2.8363	0.2065	263	0.1773	2183	2446	99
2.8363-2.9496	0.2141	254	0.181	2192	2446	99
2.9496-3.0833	0.2022	262	0.1748	2186	2448	99
3.0833-3.2452	0.2008	248	0.1684	2198	2446	99
3.2452-3.4476	0.1884	258	0.1687	2181	2439	99
3.4476-3.7122	0.1887	251	0.1634	2190	2441	99
3.7122-4.0829	0.1869	254	0.1511	2206	2460	99
4.0829-4.667	0.1513	251	0.1402	2216	2467	99
4.667-5.8551	0.1798	254	0.1588	2218	2472	99
5.8551-19.9242	0.2	252	0.18	2192	2444	97

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	1.0114	0.1035	-0.7453	3.6151	-0.582	1.3643	0.0171	0.1146	0.0741	-0.1404	0.0047	0.1805	-0.1511	0.0008	0.0028	0.2057	0.0301	-0.0714	0.178	0.0235	0.1379	29.4633	72.6426	-43.1102
2	1.6771	-0.7611	0.2411	4.6772	-0.4048	2.4009	0.0297	-0.0693	0.08	0.0699	0.0088	0.3337	-0.203	-0.1917	-0.0525	0.1187	0.0056	0.0259	0.147	-0.0057	0.1056	27.5544	65.347	-26.4926
3	3.7781	-0.355	-0.3659	6.248	-1.2766	7.4435	-0.0028	-0.0675	0.3348	0.0708	-0.1459	-0.4302	-1.052	0.2895	0.2065	0.4216	-0.0664	-0.0754	0.1674	-0.0125	0.3038	39.7382	82.3825	-30.6344
4	2.3616	-0.2741	0.6481	2.3489	-1.0846	2.5757	0.0833	-0.2992	-0.4021	0.3215	-0.144	-0.1111	0.1351	0.0674	0.0468	0.1933	0.0128	0.0014	0.1954	-0.0003	0.1729	33.3139	53.2573	-16.938
5	1.0329	-0.1774	0.1	2.2725	-0.6286	2.1539	0.0037	-0.035	0.0601	0.0539	-0.0398	-0.1112	-0.1811	0.0835	0.0296	0.1139	-0.0159	-0.0082	0.1228	-0.0008	0.1201	37.461	69.9782	-30.7332
6	1.9208	-1.4349	-0.0414	6.7347	-1.3761	2.7943	0.1106	0.2343	-0.1587	-0.4528	-0.271	-0.1274	0.4111	0.0912	0.1399	0.2253	-0.0016	0.0132	0.137	-0.0166	0.1166	42.5715	56.3443	-50.5955
7	0.9904	0.4863	-0.4852	2.7322	-0.4316	1.4941	-0.1056	0.056	-0.206	-0.2627	-0.0194	-0.0635	0.3233	-0.0919	0.1057	0.2129	-0.0148	-0.0149	0.1354	-0.0192	0.1346	35.9788	47.2522	-40.1098
8	5.3946	0.1452	-0.3498	7.0423	-0.943	7.5936	0.1496	0.5655	0.4892	-0.4042	-0.5086	-0.9721	-0.2854	0.866	0.3723	0.2519	-0.0658	0.0691	0.2868	0.0721	0.2803	50.1581	67.1194	-52.0247
9	2.8671	-0.8745	1.8531	9.1286	-6.7139	8.3311	-0.741	0.7023	0.9706	1.0839	-0.8707	-1.142	-1.7316	2.2358	1.8199	0.7351	-0.3462	-0.1438	1.2913	-0.0396	1.075	55.4457	70.7301	-40.5134
10	1.2652	-0.265	-0.3057	2.2724	0.3305	2.2077	-0.0123	0.041	-0.1351	-0.0205	-0.0559	-0.0255	0.1813	-0.0389	0.0491	0.1468	-0.0137	-0.0217	0.1174	0.0237	0.1032	36.2465	51.2826	-33.1402
11	1.7162	-0.1205	-0.2831	3.2909	0.2611	0.4696	0.005	0.1668	-0.1923	-0.1939	0.0065	0.0083	0.1274	-0.0231	-0.0143	0.1335	0.0006	-0.0216	0.1709	-0.051	0.1305	1.3845	-55.646	-5.7249
12	1.2398	1.4522	1.2683	7.635	3.468	2.132	-0.0853	0.2564	-0.0345	-0.5675	0.2979	-0.4913	-0.2241	0.3126	-0.1602	0.0949	-0.0165	0.0482	0.2175	-0.0099	0.2058	16.0361	-50.2754	-2.1677
13	1.1494	0.2074	0.2306	3.0594	0.2175	1.0072	0.0107	0.0124	-0.0649	0.0682	0.0395	-0.2239	0.0849	0.1191	-0.042	0.0645	0.0092	-0.0038	0.1427	-0.0092	0.1351	14.0909	-46.4716	9.048
14	2.7266	0.8013	2.7317	6.5202	0.1524	3.2021	0.3	-0.0822	-0.4866	0.1932	-0.0065	-0.2813	0.7923	0.4193	-0.2281	0.2551	0.0245	-0.0541	0.1877	0.0507	0.2382	9.8591	-66.0496	10.9721
15	9.2562	-0.5668	-1.2473	8.5953	3.9066	5.7151	0.0698	-0.7677	-0.3828	0.7086	-0.2569	0.8847	0.4904	-0.1309	0.1374	0.2682	-0.072	0.0113	0.2146	0.0703	0.3223	-0.4519	-65.0559	9.6465
16	2.3515	1.3952	-0.0732	3.4257	0.4533	1.7742	0.1921	-0.1422	0.1698	0.34	-0.0994	-0.237	-0.1658	0.2562	-0.0917	0.088	0.0244	-0.0135	0.1687	-0.0037	0.1849	19.647	-41.0338	11.516
17	4.5615	4.39	-5.9426	6.7882	-4.1331	8.7118	0.386	-0.7319	0.3192	0.544	-0.3257	-0.2095	-0.6495	0.4656	-0.1323	0.3322	-0.0152	-0.0516	0.2549	-0.0774	0.2944	15.7457	-29.6233	19.3147
18	1.4125	0.0498	0.0564	2.2097	0.5317	1.4978	0.0309	-0.0968	-0.0492	0.2368	-0.0465	-0.0453	0.1053	0.0377	0.0107	0.077	-0.0117	0.0029	0.122	0.0063	0.1177	7.0256	-51.2503	11.0299
19	2.1808	-1.2349	0.184	4.4009	1.1335	1.3259	0.084	0.1657	-0.0697	-0.171	-0.1218	0.3915	0.0593	-0.1394	0.0339	0.1073	-0.0176	0.0184	0.1884	0.0149	0.134	-9.5756	-49.0425	-2.4696
20	2.0239	0.6277	0.9197	5.8972	0.216	1.4971	-0.129	0.3005	0.257	-0.4538	0.1468	-0.426	-0.083	0.0827	0.0177	0.1544	-0.0301	0.0579	0.2135	0.0478	0.1251	9.1821	-30.9557	-5.8648
21	3.7484	4.1583	-3.6268	4.5385	-4.0071	3.5292	-0.2393	0.7163	0.2972	-0.6977	0.3686	0.3071	0.0809	-0.4931	-0.0644	0.1848	-0.0105	-0.0366	0.2315	0.0114	0.1894	-5.9668	-35.8427	-6.9953
22	1.2507	0.9017	-0.1456	5.2688	-0.0996	0.8978	0.103	-0.0097	0.2424	0.2152	-0.0745	0.1076	-0.165	-0.0406	-0.049	0.0785	0.016	0.0088	0.1325	0.0015	0.1582	-3.7071	-28.6445	6.3391
23	4.4259	0.5372	-0.1403	2.4788	0.0039	5.008	0.0418	-0.0646	-0.2594	0.1763	-0.2614	0.5868	0.372	-0.8438	0.0609	0.0993	-0.0535	0.0379	0.2815	-0.0241	0.3105	-19.1291	-50.2872	3.8199
24	6.1168	7.0037	5.6711	8.4559	6.692	5.333	1.125	-0.9486	-0.5863	1.7756	-0.9549	-0.0647	1.577	-1.0098	-0.1714	0.6857	-0.1447	0.0971	0.6086	0.0821	0.559	-13.5093	-54.0661	15.3645
25	1.5424	-0.0739	-0.0243	3.1914	0.393	1.8683	0.0122	-0.074	0.0941	0.1843	0.0133	0.0393	-0.0567	-0.0318	-0.0378	0.0461	-0.0038	-0.0068	0.1209	-0.0071	0.1237	-0.2823	-34.6455	7.4
26	4.3149	1.035	-1.2339	4.0035	-1.7865	5.2023	0.0722	-0.2305	0.103	0.2365	-0.1066	0.3165	-0.1634	-0.3328	0.0024	0.0773	-0.0108	0.0106	0.1159	-0.0468	0.1395	-7.1674	-29.7476	10.0037
27	3.5194	-2.1543	1.4361	5.3121	-3.9998	3.9268	-0.0706	0.3366	0.4179	0.1601	-0.2735	-0.6586	-0.2863	0.3039	0.3383	0.1122	-0.0201	0.0171	0.223	-0.0321	0.1878	18.0139	-36.7896	1.7946

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 23 )	A	2 - 23
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 53 )	A	24 - 53
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 54 through 77 )	A	54 - 77
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 78 through 134 )	A	78 - 134
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 135 through 202 )	A	135 - 202
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 203 through 217 )	A	203 - 217
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 91 )	B	2 - 91
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 92 through 110 )	B	92 - 110
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 111 through 134 )	B	111 - 134
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 135 through 217 )	B	135 - 217
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 2 through 23 )	C	2 - 23
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 24 through 36 )	C	24 - 36
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 37 through 53 )	C	37 - 53
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 54 through 64 )	C	54 - 64
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 65 through 77 )	C	65 - 77
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 78 through 110 )	C	78 - 110
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 111 through 134 )	C	111 - 134
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 135 through 192 )	C	135 - 192
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 193 through 217 )	C	193 - 217
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 2 through 23 )	D	2 - 23
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 24 through 36 )	D	24 - 36
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 37 through 91 )	D	37 - 91
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 92 through 110 )	D	92 - 110
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 111 through 134 )	D	111 - 134
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 135 through 175 )	D	135 - 175
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 176 through 192 )	D	176 - 192
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 193 through 217 )	D	193 - 217

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