PDB-3n19: XenA - reduced

ID or keywords:

Entry

Database: PDB / ID: 3n19

Title

XenA - reduced

Components

Xenobiotic reductase A

Keywords

OXIDOREDUCTASE / FMN / flavin

Function / homology

Function and homology information

NADPH dehydrogenase activity / FMN binding / NADP binding
Similarity search - Function

Biological species

Pseudomonas putida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Spiegelhauer, O. / Dobbek, H.

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: Determinants of substrate binding and protonation in the flavoenzyme xenobiotic reductase A
Authors: Spiegelhauer, O. / Werther, T. / Mende, S. / Knauer, S.H. / Dobbek, H.

History

Deposition	May 15, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 22, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Mar 5, 2014	Group: Database references
Revision 1.3	Nov 1, 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_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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Download

PDBx/mmCIF format	3n19.cif.gz	416.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3n19.ent.gz	346.5 KB	Display	PDB format
PDBx/mmJSON format	3n19.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3n19_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3n19_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3n19_validation.xml.gz	33.5 KB	Display
Data in CIF	3n19_validation.cif.gz	49.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n1/3n19 ftp://data.pdbj.org/pub/pdb/validation_reports/n1/3n19	HTTPS FTP

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Related structure data

Related structure data	3n14C 2h8xS 3l5l 4uth C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3l67-1 5n6q-d 5cpn-d 5lni-1 5ogt-3 4utk-1 2h90-1 4utj-1 3hgj-3 1z44-d 3l5l-1 5cpl-d 3l66-1 3l68-1 5nux-2 2h8x-1 5nux-4 5lnj-1 1z41-d 5nux-3 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

B: Xenobiotic reductase A

D: Xenobiotic reductase A

hetero molecules

81 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)	83.784, 158.031, 57.845
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Xenobiotic reductase A Mass: 39914.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: 86 / Gene: xenA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q3ZDM6*PLUS, NADPH dehydrogenase
#2: Chemical	ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE Mass: 458.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₃N₄O₉P
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	A SEQUENCE DATABASE REFERENCE WHICH DERIVES FROM PSEUDOMONAS PUTIDA STRAIN 86 DOES NOT CURRENTLY EXIST.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.72 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5M Ammonium Sulfate, 100mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.92 Å
Detector	Date: Apr 20, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 1.75→33.93 Å / Num. all: 78275 / Num. obs: 77884 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.5_2)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2H8X

2h8x

Resolution: 1.75→33.929 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8119 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 25.78 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2579	3894	5 %	Random
R_work	0.198	-	-	-
obs	0.201	77862	99.5 %	-
all	-	78275	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 47.308 Å² / k_sol: 0.418 e/Å³

Displacement parameters

B_iso max: 85.75 Å² / B_iso mean: 24.5968 Å² / B_iso min: 5.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.0672 Å²	-0 Å²	0 Å²
2-	-	-4.9389 Å²	-0 Å²
3-	-	-	13.0062 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→33.929 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5556	0	77	575	6208

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	5800
X-RAY DIFFRACTION	f_angle_d	1.533	7919
X-RAY DIFFRACTION	f_chiral_restr	0.088	838
X-RAY DIFFRACTION	f_plane_restr	0.009	1032
X-RAY DIFFRACTION	f_dihedral_angle_d	19.226	2027

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.75-1.8126	0.3613	375	0.2993	7117	7492	97
1.8126-1.8851	0.3097	383	0.2461	7281	7664	99
1.8851-1.9709	0.297	385	0.2217	7314	7699	100
1.9709-2.0748	0.3139	388	0.2166	7373	7761	100
2.0748-2.2048	0.2679	388	0.199	7364	7752	100
2.2048-2.375	0.2761	389	0.1908	7394	7783	100
2.375-2.6139	0.2699	391	0.1889	7429	7820	100
2.6139-2.9919	0.2515	392	0.1914	7446	7838	100
2.9919-3.7687	0.2205	395	0.178	7515	7910	100
3.7687-33.9353	0.2198	408	0.1741	7735	8143	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	0.0911	0.1033	-0.0129	0.1966	0.0081	0.2615	0.0667	0.0101	0.0222	0.0043	0.0685	0.0436	0.0617	-0.0488	-0.1077	0.1316	-0.0098	-0.0131	0.1242	-0.0084	0.0813	-16.9979	18.1556	-22.9415
2	0.0608	0.1303	-0.0953	0.3759	-0.2012	0.1418	0.0111	-0.1161	0.1029	0.0256	0.085	0.1278	0.0572	-0.0582	-0.0372	0.1199	0.0124	-0.008	0.09	-0.0484	0.1924	-5.5004	31.1075	-4.8379
3	0.4855	0.1156	-0.157	0.3246	-0.019	0.2651	0.028	-0.0059	0.1662	-0.0827	0.045	0.0925	-0.0384	0.0632	-0.0455	0.0619	-0.0041	-0.0121	0.0748	-0.0072	0.0928	-12.1002	30.5019	-7.8541
4	0.3283	0.0522	0.1062	0.2898	0.3487	0.4735	-0.0121	-0.0824	0.1904	0.0314	0.02	0.0279	0.0295	-0.0002	-0.0131	0.0876	0.0294	0.0134	0.0887	-0.0241	0.1597	-18.7064	30.6971	1.2006
5	0.3321	-0.1243	0.0411	0.0622	0.0065	0.025	-0.0101	-0.0145	0.1343	-0.0123	-0.0287	0.0507	0.0325	-0.0105	0.0206	0.0801	0.0039	0.0095	0.09	-0.0363	0.186	-30.4356	27.5337	-4.1254
6	0.2426	-0.0187	0.185	0.7072	-0.3919	0.5218	-0.0946	0.0321	0.1335	0.0771	-0.0074	0.1563	-0.1462	-0.0072	0.0314	0.0819	-0.0039	-0.0056	0.0775	-0.0025	0.1701	-27.9026	21.8138	-9.5222
7	0.1567	0.1559	-0.206	0.4815	-0.1295	0.494	-0.1693	0.056	-0.1708	0.0821	-0.0688	0.0406	-0.0327	-0.13	0.2196	0.1238	-0.0197	0.0323	0.1407	-0.0158	0.1757	-37.4007	14.7516	-6.4964
8	0.2586	0.0595	-0.05	0.1478	0.1962	0.3388	-0.0104	0.0735	-0.0838	0.0462	-0.0252	0.1094	0.1663	-0.0311	0.022	0.1328	0.0236	0.0198	0.0918	-0.0034	0.1905	-26.0838	12.8874	-6.4568
9	0.1859	-0.2418	0.0338	0.4823	0.0508	0.3028	-0.0567	0.1503	-0.095	0.013	0.0088	0.1493	0.0406	0.0068	0.0458	0.0955	-0.0098	0.0179	0.057	-0.0075	0.1246	-17.2464	10.8491	-16.0387
10	0.4094	-0.0894	0.2337	0.3069	-0.2582	0.2822	0.0104	0.0943	-0.0236	-0.0471	-0.1175	-0.1264	0.0352	0.1212	0.0695	0.1324	-0.0119	0.029	0.1302	-0.0364	0.0861	-0.5633	12.6182	-27.2889
11	0.1354	-0.1097	0.0048	0.1079	-0.0114	0.002	0.0062	-0.2751	-0.0611	0.0389	0.091	0.0612	0.0067	0.1307	-0.0854	0.1368	0.005	-0.0409	0.1693	-0.0353	0.1157	19.2707	16.1905	-4.1886
12	0.5498	0.0957	0.0835	0.3299	-0.3206	0.5288	0.007	0.0768	0.0913	-0.0097	0.0617	-0.0021	0.0497	-0.0339	-0.0369	0.0853	-0.0057	0.0117	0.0723	0.0074	0.0087	13.5657	28.5231	-24.4236
13	0.2513	-0.22	0.0775	0.2802	-0.2138	0.4721	-0.0404	0.0621	0.1771	-0.0347	-0.087	-0.1008	0.0023	0.2159	0.0936	0.0808	-0.0318	0.0112	0.164	0.0579	0.153	30.605	27.1952	-29.7278
14	0.1732	0.1018	-0.0004	0.3332	-0.1815	0.1599	0.0208	0.0839	0.0488	-0.1605	-0.0589	-0.0746	-0.1003	0.1058	0.0691	0.0884	-0.0172	0.0091	0.1498	-0.0051	0.1627	29.509	21.5131	-18.3092
15	0.4415	0.3426	0.1813	0.3041	0.0808	0.2002	0.2589	-0.1571	0.1284	-0.1114	0.0058	-0.2033	-0.0073	0.0516	-0.1686	0.0937	0.0549	0.0375	0.1921	0.0276	0.429	36.953	7.8197	-28.1021
16	0.6544	0.0776	-0.4097	0.3434	-0.2085	0.3561	-0.0003	-0.2899	0.0268	0.1325	-0.0777	-0.0629	-0.0135	0.1515	0.0178	0.0705	0.0201	-0.0012	0.1402	0.0019	0.048	34.717	17.424	-16.8915
17	0.3905	-0.0801	0.164	0.0811	0.0264	0.3281	0.0347	0.0384	-0.2683	-0.0592	0.1382	-0.1135	0.1033	0.1287	-0.1741	0.1633	-0.0021	-0.0304	0.1246	0.0152	0.2497	26.2899	7.0512	-24.815
18	0.4783	-0.4112	0.0206	0.4855	-0.143	0.5918	0.1759	-0.0654	-0.1529	-0.0458	0.019	-0.0985	0.1029	0.2579	-0.1466	0.126	0.0045	0.0286	0.1308	-0.005	0.2773	24.5531	11.0072	-16.2272
19	0.5211	-0.0281	-0.0168	0.1425	0.0506	0.055	0.0405	-0.1312	-0.3447	0.149	0.0269	-0.1009	-0.0817	-0.0022	-0.0506	0.1064	0.0183	-0.0184	0.0584	0.0313	0.2206	14.2735	9.0309	-13.0772
20	0.1409	-0.0142	-0.0925	0.0325	-0.012	0.0912	-0.1658	0.0234	-0.0414	0.007	0.0243	-0.1462	0.0635	0.0155	0.1386	0.1151	0.0558	0.0278	0.1003	-0.0034	0.2045	1.6597	12.3509	-2.6038

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain B and resid 2:24)	B	2 - 24
2	X-RAY DIFFRACTION	2	(chain B and resid 25:39)	B	25 - 39
3	X-RAY DIFFRACTION	3	(chain B and resid 40:79)	B	40 - 79
4	X-RAY DIFFRACTION	4	(chain B and resid 80:165)	B	80 - 165
5	X-RAY DIFFRACTION	5	(chain B and resid 166:219)	B	166 - 219
6	X-RAY DIFFRACTION	6	(chain B and resid 220:241)	B	220 - 241
7	X-RAY DIFFRACTION	7	(chain B and resid 242:254)	B	242 - 254
8	X-RAY DIFFRACTION	8	(chain B and resid 255:290)	B	255 - 290
9	X-RAY DIFFRACTION	9	(chain B and resid 291:336)	B	291 - 336
10	X-RAY DIFFRACTION	10	(chain B and resid 337:360)	B	337 - 360
11	X-RAY DIFFRACTION	11	(chain D and resid 2:20)	D	2 - 20
12	X-RAY DIFFRACTION	12	(chain D and resid 21:124)	D	21 - 124
13	X-RAY DIFFRACTION	13	(chain D and resid 125:218)	D	125 - 218
14	X-RAY DIFFRACTION	14	(chain D and resid 219:239)	D	219 - 239
15	X-RAY DIFFRACTION	15	(chain D and resid 240:248)	D	240 - 248
16	X-RAY DIFFRACTION	16	(chain D and resid 249:266)	D	249 - 266
17	X-RAY DIFFRACTION	17	(chain D and resid 267:293)	D	267 - 293
18	X-RAY DIFFRACTION	18	(chain D and resid 294:305)	D	294 - 305
19	X-RAY DIFFRACTION	19	(chain D and resid 306:335)	D	306 - 335
20	X-RAY DIFFRACTION	20	(chain D and resid 336:360)	D	336 - 360

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