PDB-2rg1: Crystal structure of E. coli WrbA apoprotein

ID or keywords:

Entry

Database: PDB / ID: 2rg1

Title

Crystal structure of E. coli WrbA apoprotein

Components

Flavoprotein WrbA

Keywords

OXIDOREDUCTASE /

ELECTRON TRANSPORT / quinone oxidoreductase /

flavoprotein / flavodoxin-like fold / FMN-binding

Function / homology

Function and homology information

NADPH dehydrogenase (quinone) activity /

NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity /

NAD(P)H dehydrogenase (quinone) activity / NAD binding / FMN binding /

flavin adenine dinucleotide binding /

NADP binding / response to oxidative stress / protein-containing complex ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.85 Å

Authors

Kuta Smatanova, I. / Wolfova, J. / Brynda, J. / Lapkouski, M. / Mesters, J.R. / Grandori, R. / Carey, J.

Citation

Journal: Biochim.Biophys.Acta / Year: 2009
Title: Structural organization of WrbA in apo- and holoprotein crystals.
Authors: Wolfova, J. / Smatanova, I.K. / Brynda, J. / Mesters, J.R. / Lapkouski, M. / Kuty, M. / Natalello, A. / Chatterjee, N. / Chern, S.Y. / Ebbel, E. / Ricci, A. / Grandori, R. / Ettrich, R. / Carey, J.

History

Deposition	Oct 2, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Aug 30, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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	2rg1.cif.gz	80.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2rg1.ent.gz	60.2 KB	Display	PDB format
PDBx/mmJSON format	2rg1.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/rg/2rg1 ftp://data.pdbj.org/pub/pdb/validation_reports/rg/2rg1	HTTPS FTP

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Related structure data

Related structure data	2r96SC 2r97C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1su8-d 1suf-d 6nbl-1 5e6t-d 6nbl-2 4jwu-1 4p2n-2 4udx-d 7cd9-d 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
Related items in Molecule of the Month	#133 - Jan 2011 Nitric Oxide Synthase similarity (2) #228 - Dec 2018 Directed Evolution of Enzymes similarity (2)

Deposited unit

A: Flavoprotein WrbA

B: Flavoprotein WrbA

hetero molecules

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

1

A: Flavoprotein WrbA

B: Flavoprotein WrbA

hetero molecules

A: Flavoprotein WrbA

B: Flavoprotein WrbA

hetero molecules

defined by author&software
83.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.850, 75.690, 56.550
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Flavoprotein WrbA / E.C.1.6.5.2 / Trp repressor-binding protein A Mass: 20862.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12/JM101 / Description: genomic sequence cloned in pET3a / Gene: wrbA / Plasmid: pKGWa / Production host: Escherichia coli (E. coli) / Strain (production host): CY15071(lambda-DE3) References: UniProt: P0A8G6, NAD(P)H dehydrogenase (quinone)
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.82 Å³/Da / Density % sol: 32.28 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG 4000,0.2M magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

Diffraction	Mean temperature: 200 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9776 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 20, 2007 / Details: mirrors
Radiation	Monochromator: double crystal Si(111), horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9776 Å / Relative weight: 1
Reflection	Resolution: 1.85→20 Å / Num. all: 26663 / Num. obs: 26411 / % possible obs: 99.2 % / Redundancy: 3.8 % / R_merge(I) obs: 0.061 / Χ²: 1.017 / Net I/σ(I): 21.1
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.25 / Mean I/σ(I) obs: 5.55 / Num. unique all: 1292 / Χ²: 1.144 / % possible all: 99.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R96

2r96

Resolution: 1.85→19.31 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.955 / SU B: 5.522 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.195	1000	3.8 %	RANDOM
R_work	0.171	-	-	-
all	0.172	25584	-	-
obs	0.172	25382	99.2 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 23.202 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.05 Å²	0 Å²	0 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	0.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→19.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2480	0	2	172	2654

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	2525
X-RAY DIFFRACTION	r_angle_refined_deg	1.518	1.952	3425
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.859	5	325
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.038	23.895	95
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.581	15	388
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.409	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.162	0.2	395
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1879
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	1252
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	1779
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	173
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.176	0.2	64
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.158	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	0.908	1.5	1674
X-RAY DIFFRACTION	r_mcangle_it	1.481	2.5	2604
X-RAY DIFFRACTION	r_scbond_it	3.514	5	984
X-RAY DIFFRACTION	r_scangle_it	5.409	10	821

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.227	76	-
R_work	0.201	1836	-
all	-	1912	-
obs	-	1836	99.95 %

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	7.1192	-1.0386	0.2115	3.4705	-0.1519	5.0136	-0.0145	0.4316	-0.2432	-0.2638	0.0233	0.1653	0.0376	-0.0306	-0.0087	-0.0873	-0.0572	-0.0059	-0.0704	-0.051	-0.116	-10.1603	17.9674	1.0284
2	7.0147	-0.8699	3.8099	4.9015	2.2805	16.3073	-0.0372	0.3586	0.673	-0.3955	-0.2087	0.7432	-0.8046	-0.4127	0.2459	-0.0614	-0.0262	-0.0205	0.0724	-0.0185	0.0974	-21.1402	21.4976	3.8821
3	3.1667	0.0596	0.7261	0.0029	-0.0455	2.1641	0.0302	-0.0534	-0.2953	-0.0407	-0.0343	0.193	0.1616	-0.2243	0.0041	-0.0667	-0.0124	0.0181	-0.0795	-0.0252	-0.0885	-10.2009	18.2428	10.5825
4	9.7388	4.4468	-5.1303	46.2984	-3.9937	2.7642	0.3414	0.0512	0.0043	-0.1632	-0.0204	0.9521	-0.472	-0.1735	-0.321	-0.0204	0.0171	0.0098	-0.0906	-0.0054	-0.077	-12.3916	36.822	8.821
5	2.9078	3.7654	-2.6479	16.6564	-7.2276	7.34	0.0316	-0.1871	0.3597	0.1443	-0.0642	0.5093	-0.1196	0.0548	0.0327	-0.0914	0.0158	-0.0114	-0.0871	-0.0426	-0.045	-16.2868	27.7171	12.274
6	2.2675	0.0921	-0.9212	1.7336	-2.4553	6.3936	0.0364	-0.1846	0.012	0.0806	0.0753	0.2069	0.0226	-0.2254	-0.1117	-0.0981	-0.0523	-0.0073	-0.0912	-0.0161	-0.087	-8.3334	20.1789	17.565
7	27.3273	22.0295	23.9693	20.7885	16.9832	22.8301	-1.2774	1.3219	1.2331	-1.7879	0.4385	0.2127	-1.1891	0.4122	0.8389	0.1253	0.0254	0.0264	0.0313	0.0664	0.0709	-5.6879	35.9386	2.4483
8	1.168	-1.5194	1.4527	2.7496	-3.9898	7.5112	-0.0586	-0.0521	0.0736	0.2463	0.1093	0.1937	-0.4157	-0.2729	-0.0507	-0.1035	0.0037	-0.0057	-0.0796	-0.0039	-0.0871	-3.793	27.6685	15.0897
9	8.5852	-0.8573	3.6555	6.0426	-0.6321	5.9025	-0.1428	1.0231	0.5716	-0.7513	-0.1594	0.0146	-0.3327	0.2847	0.3022	0.0353	-0.0146	-0.0106	-0.0124	0.026	-0.0826	0.2699	29.08	0.9962
10	5.0178	-3.7152	3.8654	12.3541	-7.8717	10.7663	0.0071	0.4375	-0.224	-0.4738	0.1033	-0.1151	0.3752	0.1823	-0.1104	-0.1129	-0.0426	0.0243	-0.01	-0.0935	-0.0741	0.0918	19.1355	-0.4512
11	3.5905	2.1256	0.3834	5.7757	0.6683	6.1716	0.0699	-0.2033	-0.049	0.2122	-0.0872	-0.2755	0.002	0.1469	0.0173	-0.1504	0.0368	-0.0306	-0.0838	0.0264	-0.0987	17.4979	23.7464	27.574
12	6.8366	1.2663	-0.3034	7.3533	-2.9207	6.8214	-0.0674	0.2485	0.4736	0.1844	-0.2534	-0.4188	-0.381	0.5888	0.3209	-0.1013	0.0162	-0.0424	-0.0101	0.0511	0.0768	25.2845	29.3027	22.8071
13	9.23	4.7953	3.1238	21.936	-2.8741	20.5455	-0.4768	0.6706	0.0438	0.0036	-0.1079	-0.1985	-0.2553	1.8245	0.5847	-0.0299	0.0307	0.0047	0.1178	0.0334	-0.0196	23.1285	22.5431	13.4053
14	6.4775	-2.4565	-1.136	9.1077	4.1893	5.2079	0.106	-0.0067	0.8456	-0.1988	-0.1617	-0.4785	-0.5186	-0.1778	0.0556	-0.0631	0.0394	-0.0204	-0.1036	0.0061	-0.0572	13.1389	32.566	21.2775
15	6.9025	-1.406	-0.6938	6.8051	2.016	11.3519	-0.122	0.0439	0.1769	0.1189	0.0554	0.2551	0.0198	-0.6462	0.0666	-0.0141	-0.0073	-0.0237	-0.0802	0.0257	0.0053	16.8585	37.0898	16.9227
16	3.2042	0.0927	-0.9042	1.0968	-0.3942	8.7523	0.0169	0.1772	0.169	-0.089	0.0411	-0.2259	-0.3297	0.2249	-0.0581	-0.1157	0.0248	-0.0125	-0.1111	-0.0201	-0.0766	14.4781	27.3569	12.3408
17	14.0443	11.0667	19.2572	37.6452	32.7919	43.0059	-1.7069	-0.8948	1.9632	0.0243	1.3123	1.6106	-2.269	-0.5012	0.3946	0.2852	0.1402	-0.0276	0.1142	-0.111	0.3512	4.9054	39.7174	27.0858
18	3.026	0.4172	-1.0147	2.1799	0.1643	5.35	-0.0317	-0.0114	0.2492	0.1594	0.1016	-0.0348	-0.2609	-0.0507	-0.0699	-0.119	0.0302	-0.0175	-0.1302	-0.0062	-0.0818	6.0521	28.7336	16.222
19	5.6629	-0.7512	2.3045	0.7225	-0.5621	6.8157	-0.191	-0.7679	0.2877	0.3101	0.0731	0.1059	-0.3881	-0.4158	0.1179	-0.0472	0.0282	-0.0119	-0.0096	-0.0259	-0.0859	6.7521	25.5978	31.4596
20	13.1358	-4.5826	-0.1295	22.6463	8.4791	21.6028	0.0927	0.7683	-0.7313	-1.3711	-0.107	0.2249	0.6959	0.4401	0.0144	0.0422	0.0084	-0.0341	-0.0917	-0.0176	-0.0294	10.552	12.0392	17.6045

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 38	2 - 39
2	X-RAY DIFFRACTION	2	A	A	39 - 62	40 - 63
3	X-RAY DIFFRACTION	3	A	A	63 - 77	64 - 78
4	X-RAY DIFFRACTION	4	A	A	78 - 82	79 - 83
5	X-RAY DIFFRACTION	5	A	A	83 - 90	84 - 91
6	X-RAY DIFFRACTION	6	A	A	91 - 111	92 - 112
7	X-RAY DIFFRACTION	7	A	A	112 - 120	113 - 121
8	X-RAY DIFFRACTION	8	A	A	121 - 136	122 - 137
9	X-RAY DIFFRACTION	9	A	A	137 - 171	138 - 172
10	X-RAY DIFFRACTION	10	A	A	172 - 196	173 - 197
11	X-RAY DIFFRACTION	11	B	B	1 - 32	2 - 33
12	X-RAY DIFFRACTION	12	B	B	33 - 62	34 - 63
13	X-RAY DIFFRACTION	13	B	B	63 - 68	64 - 69
14	X-RAY DIFFRACTION	14	B	B	69 - 80	70 - 81
15	X-RAY DIFFRACTION	15	B	B	81 - 91	82 - 92
16	X-RAY DIFFRACTION	16	B	B	92 - 113	93 - 114
17	X-RAY DIFFRACTION	17	B	B	114 - 120	115 - 121
18	X-RAY DIFFRACTION	18	B	B	121 - 142	122 - 143
19	X-RAY DIFFRACTION	19	B	B	143 - 187	144 - 188
20	X-RAY DIFFRACTION	20	B	B	188 - 197	189 - 198

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