PDB-4jic: Glycerol Trinitrate Reductase NerA from Agrobacterium radiobacter

ID or keywords:

Entry

Database: PDB / ID: 4jic

Title

Glycerol Trinitrate Reductase NerA from Agrobacterium radiobacter

Components

GTN Reductase

Keywords

OXIDOREDUCTASE /

TIM-barrel / ene-reductase

Function / homology

Function and homology information

FMN binding /

oxidoreductase activity
Similarity search - Function

Biological species

Agrobacterium tumefaciens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Oberdorfer, G. / Gruber, K.

Citation

Journal: Chembiochem / Year: 2013
Title: The Structure of Glycerol Trinitrate Reductase NerA from Agrobacterium radiobacter Reveals the Molecular Reason for Nitro- and Ene-Reductase Activity in OYE Homologues.
Authors: Oberdorfer, G. / Binter, A. / Wallner, S. / Durchschein, K. / Hall, M. / Faber, K. / Macheroux, P. / Gruber, K.

History

Deposition	Mar 5, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2013	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	4jic.cif.gz	465.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4jic.ent.gz	378.3 KB	Display	PDB format
PDBx/mmJSON format	4jic.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ji/4jic ftp://data.pdbj.org/pub/pdb/validation_reports/ji/4jic	HTTPS FTP

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Related structure data

Related structure data	4jipC 4jiqC 1h50S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3g5a-1 6dq9-d 4o93-1 6bh2-d 5i5d-1 6vat-5 5f3c-3 6yi1-2 6dqe-d 3m51-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4jipC

4jiqC

1h50S

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: GTN Reductase

B: GTN Reductase

C: GTN Reductase

hetero molecules

123 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GTN Reductase

hetero molecules

defined by author&software
41.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: GTN Reductase

hetero molecules

defined by author&software
41.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: GTN Reductase

hetero molecules

defined by author&software
41.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.446, 93.018, 180.496
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	GTN Reductase Mass: 40567.980 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: nerA / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31246
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1869 / 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: 293 K / Method: microbatch / pH: 6 Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS, 25% w/v polyethylene glycol 3,350, pH 6.0, Microbatch, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9724 Å / Relative weight: 1
Reflection	Resolution: 1.6→90.248 Å / Num. all: 151990 / Num. obs: 149769 / % possible obs: 98.53 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / R_sym value: 0.107 / Net I/σ(I): 7
Reflection shell	Resolution: 1.6→1.69 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.3 / R_sym value: 0.413 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
DNA		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Pdb entry 1h50

1h50

Resolution: 1.6→38.468 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 18.78 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1895	7523	5.03 %	RANDOM
R_work	0.1587	-	-	-
obs	0.1603	149648	98.47 %	-
all	-	151990	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 30.494 Å² / k_sol: 0.322 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.1598 Å²	0 Å²	-0 Å²
2-	-	2.4163 Å²	-0 Å²
3-	-	-	-0.2566 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→38.468 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8397	0	115	1869	10381

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	9019
X-RAY DIFFRACTION	f_angle_d	1.073	12351
X-RAY DIFFRACTION	f_dihedral_angle_d	13.755	3363
X-RAY DIFFRACTION	f_chiral_restr	0.071	1334
X-RAY DIFFRACTION	f_plane_restr	0.005	1657

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 (%)
1.6-1.6192	0.291	258	0.2684	4448	X-RAY DIFFRACTION	95
1.6192-1.6383	0.2722	265	0.2526	4693	X-RAY DIFFRACTION	98
1.6383-1.6582	0.2341	241	0.2238	4644	X-RAY DIFFRACTION	98
1.6582-1.6792	0.2277	232	0.2063	4736	X-RAY DIFFRACTION	99
1.6792-1.7013	0.2291	268	0.2024	4665	X-RAY DIFFRACTION	98
1.7013-1.7246	0.2292	260	0.1953	4695	X-RAY DIFFRACTION	99
1.7246-1.7493	0.2491	248	0.1914	4692	X-RAY DIFFRACTION	99
1.7493-1.7754	0.2063	238	0.1804	4712	X-RAY DIFFRACTION	99
1.7754-1.8031	0.2168	264	0.1706	4729	X-RAY DIFFRACTION	99
1.8031-1.8327	0.1968	250	0.1634	4668	X-RAY DIFFRACTION	99
1.8327-1.8643	0.1879	238	0.1522	4752	X-RAY DIFFRACTION	99
1.8643-1.8982	0.1801	253	0.1567	4720	X-RAY DIFFRACTION	99
1.8982-1.9347	0.2064	230	0.1599	4708	X-RAY DIFFRACTION	99
1.9347-1.9742	0.1901	229	0.1475	4759	X-RAY DIFFRACTION	99
1.9742-2.0171	0.1765	247	0.1477	4774	X-RAY DIFFRACTION	99
2.0171-2.064	0.2047	227	0.1564	4775	X-RAY DIFFRACTION	99
2.064-2.1156	0.2134	234	0.1636	4722	X-RAY DIFFRACTION	99
2.1156-2.1728	0.1922	254	0.1562	4729	X-RAY DIFFRACTION	99
2.1728-2.2368	0.2019	266	0.151	4734	X-RAY DIFFRACTION	99
2.2368-2.3089	0.1779	248	0.1459	4806	X-RAY DIFFRACTION	99
2.3089-2.3915	0.19	238	0.1513	4759	X-RAY DIFFRACTION	99
2.3915-2.4872	0.183	263	0.1527	4764	X-RAY DIFFRACTION	99
2.4872-2.6004	0.1959	252	0.156	4793	X-RAY DIFFRACTION	99
2.6004-2.7374	0.1886	244	0.152	4841	X-RAY DIFFRACTION	99
2.7374-2.9089	0.1651	287	0.1512	4752	X-RAY DIFFRACTION	99
2.9089-3.1334	0.1785	247	0.1481	4803	X-RAY DIFFRACTION	99
3.1334-3.4485	0.1807	263	0.1477	4802	X-RAY DIFFRACTION	98
3.4485-3.9471	0.1525	268	0.1408	4759	X-RAY DIFFRACTION	98
3.9471-4.9713	0.154	260	0.1301	4813	X-RAY DIFFRACTION	97
4.9713-38.4796	0.171	251	0.1585	4878	X-RAY DIFFRACTION	95

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	0.3998	-0.0082	-0.0327	0.2897	0.0547	0.2798	0.0072	-0.0295	0.0286	0.0012	-0.0057	0.0267	-0.0318	-0.0305	-0.0059	0.0381	0.003	-0.002	0.0358	-0.0016	0.0404	-3.9422	59.3059	99.6621
2	2.646	-0.7472	-0.6044	2.8916	-0.0516	0.5536	0.0702	0.1903	0.2649	-0.2534	-0.0204	0.5042	-0.5265	-0.5097	-0.0355	0.2912	0.1596	-0.051	0.3931	-0.0478	0.2627	1.2747	67.9703	81.5729
3	0.1602	0.5669	0.2373	3.0078	0.2916	0.6516	0.0893	0.2561	0.0221	-0.2163	-0.0457	0.6134	-0.2256	-0.5086	-0.0535	0.3721	0.2473	-0.1481	0.4399	-0.0438	0.2895	1.4592	66.1851	79.5574
4	0.3908	-0.0011	0.0339	0.2263	-0.0225	0.2732	0.0022	-0.0148	-0.046	-0.0134	-0.0029	0.0098	0.0208	0.0149	0.0005	0.0511	-0.0007	0.0001	0.0367	-0.0018	0.039	3.8938	48.9331	98.2762
5	0.5455	-0.0315	-0.0158	0.487	0.0662	0.4267	-0.0007	-0.0623	-0.0851	0.0202	-0.0106	-0.034	0.0453	0.0641	0.0055	0.0417	0.0115	0.0072	0.0457	0.0121	0.0358	36.9069	33.7844	129.2545
6	2.4008	-0.2219	-0.0836	1.9029	-0.3058	0.0779	-0.0598	0.2613	-0.2978	-0.1854	0.0054	-0.4472	0.3533	0.4894	0.0302	0.0259	0.1704	0.0807	0.2805	-0.0677	0.0832	29.9944	27.5482	111.1176
7	0.3648	-0.12	0.0992	0.3598	0.1006	0.6297	-0.0127	-0.0103	-0.0229	0.0123	-0.0214	0.0442	0.016	-0.0168	0.0326	0.0443	0.0026	0.0121	0.0449	0.0024	0.0458	21.6052	42.1421	129.7572
8	0.7483	-0.2534	-0.4426	0.6234	0.0793	0.5897	0.0268	-0.0232	0.0853	-0.052	0.0132	-0.1139	-0.0435	0.0933	-0.0267	0.0471	-0.0133	0.0021	0.0712	0.0002	0.0557	43.3897	48.6332	124.4083
9	0.5452	0.0344	-0.158	0.2586	0.0412	0.4601	0.0097	0.0092	0.0615	-0.021	-0.0032	-0.0315	-0.0368	0.0329	-0.0075	0.0462	-0.0034	0.0042	0.0431	-0.0055	0.0561	2.3492	12.9505	110.4702
10	2.1312	1.3125	-0.2822	2.2801	-0.082	0.0432	0.2424	-0.3685	0.1052	0.2912	-0.1032	-0.374	-0.1829	0.1962	-0.1266	0.1396	-0.0722	-0.017	0.2182	0.0295	0.2148	-6.3409	15.4258	128.9106
11	1.4389	1.2421	-0.2653	2.5834	-0.3882	1.0201	0.1595	-0.063	0.2608	-0.0854	0.0738	-0.3414	-0.1069	-0.0251	-0.1891	0.318	-0.097	-0.0334	0.2004	-0.0151	0.3428	-1.8973	25.3264	130.4081
12	0.4365	0.0666	0.0006	0.3655	0.0942	0.345	-0.0051	-0.0124	-0.0099	0.0076	-0.0021	-0.0068	0.0169	0.0028	0.0073	0.0487	0.0015	0.0034	0.041	-0.0012	0.0319	-5.1185	2.1323	111.9653

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 2:124)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 125:135)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 136:141)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 142:371)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 2:122)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 123:141)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 142:292)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 293:371)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 2:124)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 125:129)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 130:141)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 142:371)

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