PDB-4ywn: Crystal structure of NADH-FMN oxidoreductase from Mycobacterium avium

ID or keywords:

Entry

Database: PDB / ID: 4ywn

Title

Crystal structure of NADH-FMN oxidoreductase from Mycobacterium avium

Components

NADH-fmn oxidoreductase

Keywords

OXIDOREDUCTASE / SSGCID /

Mycobacterium avium / NADH-fmn oxidoreductase /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

Biological species

Mycobacterium avium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of NADH-FMN oxidoreductase from Mycobacterium avium
Authors: Abendroth, J. / Jensen, M. / Arakaki, T.L. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Mar 20, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 1, 2015	Provider: repository / Type: Initial release
Revision 1.1	Aug 26, 2015	Group: Experimental preparation
Revision 1.2	Nov 22, 2017	Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3	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

-
Download

PDBx/mmCIF format	4ywn.cif.gz	124.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4ywn.ent.gz	95.6 KB	Display	PDB format
PDBx/mmJSON format	4ywn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	3pftS S: Starting model for refinement
Similar structure data	1ifq-d 1dgv-d 3brs-2 3lte-7 6ljn-d 2zgt-d 3gv0-d 1gef-2 3t5x-d 6gq0-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
Other databases	TargetTrack: MyavA.00250.a

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: NADH-fmn oxidoreductase

B: NADH-fmn oxidoreductase

hetero molecules

35 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)	50.260, 50.260, 229.590
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	NADH-fmn oxidoreductase Mass: 17425.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_4912 / Plasmid: MyavA.00250.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QM95, UniProt: A0A0J9X290*PLUS
#2: Chemical	ChemComp-FLC / CITRATE ANION / Citric acid Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₅O₇
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 41 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 20 mg/mL MyavA.00250.a.A1.PS00591 against JCSG a3 (optimization: 22% PEG3350, 200 mM ammonium citrate dibasic), cryoprotectant: 20% ethylene glycol, tray 247348, puck wuf3-10

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 18, 2015

Radiation

Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. all: 28629 / Num. obs: 28598 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / B_iso Wilson estimate: 24.69 Å² / R_merge F obs: 0.998 / R_merge(I) obs: 0.072 / R_rim(I) all: 0.075 / Χ²: 0.97 / Net I/σ(I): 20.56 / Num. measured all: 335089

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.8-1.85		12	0.979	0.472	4.93	24556	2044	2041	0.493	99.9
1.85-1.9			0.983	0.378	6.24	24002	2009	2009	0.395	100
1.9-1.95			0.989	0.3	7.65	23275	1945	1945	0.314	100
1.95-2.01			0.994	0.223	9.78	23078	1942	1939	0.233	99.8
2.01-2.08			0.995	0.18	11.76	21960	1833	1833	0.188	100
2.08-2.15			0.995	0.162	13.37	21228	1777	1777	0.17	100
2.15-2.23			0.997	0.139	15.32	20644	1734	1734	0.145	100
2.23-2.32			0.995	0.115	18.1	19898	1667	1667	0.121	100
2.32-2.43			0.997	0.104	20.21	19101	1610	1610	0.109	100
2.43-2.55			0.997	0.091	22.29	18360	1555	1553	0.095	99.9
2.55-2.68			0.999	0.08	25.89	17371	1464	1464	0.084	100
2.68-2.85			0.998	0.072	28.21	16549	1413	1412	0.076	99.9
2.85-3.04			0.998	0.067	31.36	15443	1320	1320	0.07	100
3.04-3.29			0.998	0.06	35.61	14373	1240	1239	0.063	99.9
3.29-3.6			0.998	0.056	38.03	13408	1167	1167	0.059	100
3.6-4.02			0.998	0.054	39.79	11855	1040	1040	0.056	100
4.02-4.65			0.998	0.052	41.42	10763	959	959	0.055	100
4.65-5.69			0.998	0.052	40.65	8892	813	813	0.054	100
5.69-8.05			0.998	0.052	39.15	6898	664	662	0.055	99.7
	8.05		0.996	0.05	35.35	3435	433	414	0.054	95.6

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	1.8 Å	46.04 Å
Translation	1.8 Å	46.04 Å

-
Processing

Software

Name	Classification
XDS	data scaling
XSCALE	data scaling
PHASER	phasing
ARP	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3PFT

3pft

Resolution: 1.8→37.812 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2153	1427	5.02 %	Random selection
R_work	0.1788	27018	-	-
obs	0.1806	28445	99.75 %	-

Solvent computation

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

Displacement parameters

B_iso max: 98.74 Å² / B_iso mean: 36.0889 Å² / B_iso min: 14.77 Å²

Refinement step

Cycle: final / Resolution: 1.8→37.812 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2016	0	13	125	2154
B_iso mean	-	-	55.49	41.48	-
Num. residues	-	-	-	-	279

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2129
X-RAY DIFFRACTION	f_angle_d	0.993	2932
X-RAY DIFFRACTION	f_chiral_restr	0.049	367
X-RAY DIFFRACTION	f_plane_restr	0.004	378
X-RAY DIFFRACTION	f_dihedral_angle_d	11.695	754

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 (%)
1.8001-1.8644	0.2503	128	0.2035	2642	X-RAY DIFFRACTION	100
1.8644-1.939	0.2511	134	0.1954	2643	X-RAY DIFFRACTION	100
1.939-2.0273	0.2389	125	0.1851	2631	X-RAY DIFFRACTION	99
2.0273-2.1342	0.2714	149	0.1896	2635	X-RAY DIFFRACTION	100
2.1342-2.2679	0.2023	135	0.1869	2679	X-RAY DIFFRACTION	100
2.2679-2.4429	0.2295	132	0.1902	2685	X-RAY DIFFRACTION	100
2.4429-2.6887	0.2175	157	0.1874	2671	X-RAY DIFFRACTION	100
2.6887-3.0776	0.2332	150	0.1972	2718	X-RAY DIFFRACTION	100
3.0776-3.8769	0.2242	156	0.1653	2780	X-RAY DIFFRACTION	100
3.8769-50	0.1814	161	0.1664	2934	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	3.3691	1.021	-0.947	1.9917	-0.8008	3.1242	-0.3697	0.7275	-0.2893	-0.7105	0.5851	-0.1881	0.4368	-0.4966	-0.1292	0.5022	-0.1476	0.0598	0.3564	-0.0321	0.2721	18.7154	-2.3569	32.416
2	5.036	0.5412	-4.2299	1.2915	-0.0509	9.4567	-0.0632	-0.0662	-0.0542	0.1774	0.075	0.1446	-0.2317	-0.7369	0.0355	0.1917	0.0616	-0.0099	0.2394	0.0454	0.1862	16.9693	3.9894	44.7058
3	5.6549	1.3735	-0.5305	2.3209	0.5046	6.4228	-0.2226	0.3835	0.2275	0.3341	0.2103	0.2851	-0.6925	-1.0127	0.0304	0.3612	0.1388	0.0257	0.2571	0.1038	0.1987	15.7076	8.8364	42.3934
4	5.0764	1.5649	1.1091	3.1831	3.1479	3.4381	-0.0351	0.2864	-0.5031	-0.7763	0.3553	-0.1066	-0.1858	0.1755	-0.3648	0.3284	0.0474	-0.0016	0.1712	-0.0112	0.2182	20.6111	-3.8056	42.507
5	2.6736	0.4246	0.0216	1.4409	1.25	7.1527	0.1056	-0.1447	-0.1575	0.2763	-0.0251	-0.0935	0.3628	-0.276	-0.112	0.2107	0.0162	-0.0174	0.16	0.0196	0.1982	19.5317	-0.8697	51.334
6	7.179	-1.2695	1.6953	4.0249	-0.0613	8.2874	-0.1764	-0.0167	0.1826	-0.0716	0.212	0.0161	-1.0376	-0.6262	-0.0659	0.2383	-0.0109	0.0765	0.1945	0.0025	0.1764	20.298	8.8919	39.3894
7	3.3464	-0.225	4.2652	0.3645	-1.2804	7.9427	-0.9748	-1.4696	-0.6735	0.5117	0.996	-0.0812	0.81	0.1794	0.0356	0.7832	0.3428	0.0606	0.6894	0.0791	0.5803	32.758	-0.3578	38.0103
8	1.9909	0.3841	-0.3664	1.6589	2.0907	3.0622	0.0744	0.0125	0.2163	-0.4378	-0.0069	-0.1254	0.108	-0.1308	-0.0436	0.1779	-0.0129	0.0382	0.1815	0.0414	0.2199	29.0688	8.5795	15.074
9	2.7537	0.9172	-2.2147	4.7914	-2.52	3.2012	-0.335	0.1572	-0.0489	-0.3965	0.021	-0.3258	-0.0189	-0.2037	0.1968	0.214	-0.08	-0.0201	0.2213	-0.0259	0.1443	28.1637	8.775	19.1318
10	3.0204	3.4782	-1.0627	7.9098	-1.2636	5.9436	0.0868	0.0255	-0.2015	0.0066	-0.0376	0.065	0.1867	-0.6093	-0.1263	0.162	-0.0216	0.0432	0.2081	-0.0101	0.1232	22.3666	6.6269	26.0443
11	6.759	1.966	4.7906	4.5012	2.753	4.3659	-0.645	-0.1744	0.4249	-0.3738	0.1835	0.0135	-1.2245	-0.1075	0.4958	0.4231	-0.0068	0.006	0.2668	0.0444	0.2305	27.9524	17.4649	17.9413
12	6.3677	-4.568	3.9936	3.5718	-4.0389	7.6106	-0.4435	-0.5429	-0.1324	0.2355	0.4798	-0.3046	0.279	-0.0242	-0.0271	0.2587	0.0472	-0.0248	0.2152	-0.0007	0.249	31.7683	0.6855	21.7832
13	2.2784	-3.2111	3.1094	5.0057	-4.8567	4.6708	0.1652	0.7197	0.0769	-0.0578	-0.4191	-0.1568	-0.4607	1.0862	0.3207	0.3004	0.0535	0.0505	0.4314	0.0099	0.3369	39.6079	1.6821	17.8163
14	6.6694	-2.0032	0.9644	5.5241	0.4079	7.9644	0.1927	0.4528	0.1091	0.047	-0.1331	-0.2502	0.1562	0.5839	-0.0737	0.1672	0.0083	-0.0011	0.1786	0.0072	0.1589	28.791	4.0268	8.6298
15	2.3048	-0.2982	-1.6901	6.8318	4.1967	9.4441	-0.2257	-0.0735	-0.1376	-0.0434	0.2372	0.2392	0.1621	-1.0644	0.1267	0.1857	-0.0403	-0.024	0.3274	0.048	0.1827	21.5187	4.3412	16.348
16	8.0085	1.5548	1.6899	5.211	2.1	2.5377	0.0467	0.4665	0.9027	0.1011	-0.1095	0.2143	-0.9058	0.2401	-0.1524	0.3596	-0.0029	0.0372	0.2921	0.0058	0.1904	25.2953	15.9425	30.1398
17	3.0234	-0.0045	-0.4668	6.3993	-0.1461	2.8809	-0.1201	-0.0316	-0.1193	-0.605	0.0237	0.4268	-0.2528	-0.7655	0.1555	0.1486	-0.0346	0.0176	0.2645	0.0402	0.167	21.2494	6.8491	21.7239
18	9.9045	0.6879	-0.4552	6.8272	1.7122	9.0886	-0.0859	0.1077	-1.189	-0.3758	-0.2614	1.019	1.2678	0.1563	0.2339	0.9686	0.0136	-0.1329	0.2852	-0.0349	0.5705	28.1797	-9.5924	15.974

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 31 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 47 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 48 through 72 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 73 through 83 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 84 through 123 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 124 through 145 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 12 through 22 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 23 through 31 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 32 through 47 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 48 through 58 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 59 through 72 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 73 through 83 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 84 through 94 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 95 through 116 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 117 through 123 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 124 through 131 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 132 through 144 )	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 145 through 152 )	B

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
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

-
Phasing

-
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

-
Yorodumi

-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

-Phasing

-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

-Yorodumi

-
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

-
Phasing

-
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

-
Yorodumi