PDB-5lmc: Oxidized flavodiiron core of Escherichia coli flavorubredoxin, in...

Basic information

• Entry: Database: PDB / ID: 5lmc
• Title: Oxidized flavodiiron core of Escherichia coli flavorubredoxin, including the Fe-4SG atoms from its rubredoxin domain
• Components: Anaerobic nitric oxide reductase flavorubredoxin
• Keywords: OXIDOREDUCTASE / Flavorubredoxin / flavodiiron protein / diiron center / nitric oxide reductase

Function / homology

Function:

nitric oxide reductase activity / nitric oxide catabolic process / oxidoreductase activity, acting on other nitrogenous compounds as donors / response to nitric oxide / FMN binding / electron transfer activity / iron ion binding / protein-containing complex / identical protein binding / cytoplasm

Domain/homology:

Anaerobic nitric oxide reductase flavorubredoxin / Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Flavodoxin domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Flavoprotein-like superfamily / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

ACETIC ACID / CACODYLATE ION / : / MU-OXO-DIIRON / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Anaerobic nitric oxide reductase flavorubredoxin

• Biological species: Escherichia coli K-12 (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
• Authors: Romao, C.V. / Borges, P.T. / Vicente, J.B. / Carrondo, M.A. / Teixeira, M. / Frazao, C.
• Citation: Journal: J.Mol.Biol. / Year: 2016; Title: Structure of Escherichia coli Flavodiiron Nitric Oxide Reductase.; Authors: Romao, C.V. / Vicente, J.B. / Borges, P.T. / Victor, B.L. / Lamosa, P. / Silva, E. / Pereira, L. / Bandeiras, T.M. / Soares, C.M. / Carrondo, M.A. / Turner, D. / Teixeira, M. / Frazao, C.

History

Deposition	Jul 29, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 19, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 30, 2016	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Advisory / Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Assembly

Deposited unit

A: Anaerobic nitric oxide reductase flavorubredoxin

hetero molecules

Summary:

• 55.4 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	55,412	9
Polymers	54,293	1
Non-polymers	1,119	8
Water	7,134	396

1

A: Anaerobic nitric oxide reductase flavorubredoxin

hetero molecules

A: Anaerobic nitric oxide reductase flavorubredoxin

hetero molecules

A: Anaerobic nitric oxide reductase flavorubredoxin

hetero molecules

A: Anaerobic nitric oxide reductase flavorubredoxin

hetero molecules

Summary:

• defined by author
• 222 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	221,648	36
Polymers	217,172	4
Non-polymers	4,476	32
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	4_665	-x+1,-y+1,z	1
crystal symmetry operation	7_556	y,x,-z+1	1
crystal symmetry operation	10_666	-y+1,-x+1,-z+1	1

2

A: Anaerobic nitric oxide reductase flavorubredoxin

hetero molecules

A: Anaerobic nitric oxide reductase flavorubredoxin

hetero molecules

Summary:

• defined by software
• 111 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	110,824	18
Polymers	108,586	2
Non-polymers	2,238	16
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	10_666	-y+1,-x+1,-z+1	1

Calculated values:

Buried area	7930 Å2
ΔGint	-120 kcal/mol
Surface area	29280 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	150.471, 150.471, 95.361
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	177
Space group name H-M	P622

Components on special symmetry positions

ID	Model	Components
1	1	A-806- HOH
2	1	A-987- HOH
3	1	A-996- HOH

Components

Protein , 1 types, 1 molecules A

#1: Protein

A Anaerobic nitric oxide reductase flavorubredoxin / FlavoRb / Flavodiiron nitric oxide reductase

Details:

Mass: 54293.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Flavorubredoxin was modeled from residue 2 to 400, because residues 401 to 479 were not visible due to disorder. However, the heavier atoms from the missing C-terminal rubredoxin domain, Fe-4S, were detected and validated through its stereochemistry.
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: norV, flrD, ygaI, ygaJ, ygaK, b2710, JW2680 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46877

Non-polymers , 8 types, 404 molecules

#2: Chemical

A-501 ChemComp-FEO / MU-OXO-DIIRON

Details:

Mass: 127.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe₂O

#3: Chemical

A-502 ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE

Details:

Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P

#4: Chemical

A-503 A-504 ChemComp-PO4 / PHOSPHATE ION

Details:

Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄

#5: Chemical

A-505 ChemComp-CAC / CACODYLATE ION / dimethylarsinate

Details:

Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆AsO₂

#6: Chemical

A-506 ChemComp-ACY / ACETIC ACID

Details:

Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O₂

#7: Chemical

A-507 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Details:

Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃

#8: Chemical

A-508 ChemComp-FE / FE (III) ION

Details:

Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe

#9: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.87 ų/Da / Density % sol: 57.14 %
• Crystal grow: Temperature: 304 K / Method: vapor diffusion, hanging drop / pH: 6.5 ; Details: 1.0 UL OF PROTEIN AT15 MG/ML WITH 0.8 UL OF CRYSTALLIZATION SOLUTION (0.2M NA-CACODYLATE PH 6.5, 0.2 M MG-ACETATE, 20% PEG8000) and 0.2 UL OF 0.1 MOLAR HEXAMINE COBALT (III).

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9722 Å
• Detector: Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2008
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9722 Å / Relative weight: 1
• Reflection: Resolution: 1.9→59.07 Å / Num. obs: 49678 / % possible obs: 98.6 % / Redundancy: 9.8 % / B_iso Wilson estimate: 24 Ų / R_sym value: 0.119 / Net I/σ(I): 46.5
• Reflection shell: Resolution: 1.9→2.02 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.7 / CC_1/2: 0.65 / % possible all: 92.7

Processing

Software

Name	Version	Classification
PHENIX	1.6.1_357	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure: FOURIER SYNTHESIS
Starting model: 4d02

4d02

Resolution: 1.9→59.07 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.17
Details: FLAVORUBREDOXIN WAS MODELED FROM RESIDUE 2 TO 400, BECAUSE RESIDUES 401 TO 479 WERE NOT VISIBLE DUE TO DISORDER. HOWEVER, THE HEAVIER ATOMS FROM THE MISSING C-TERMINAL RUBREDOXIN DOMAIN, FE-4S, WERE DETECTED AND VALIDATED THROUGH ITS STEREOCHEMISTRY. FLAVORUBREDOXIN REFINEMENT CONVERGED TO RWORK AND RFREE OF 0.169 AND 0.185, RESPECTIVELY, USING A RFREE TEST SET SIZE OF 3.32% (1648 REFLECTIONS). THE FINAL MODEL THEN WAS REFINED VERSUS THE FULL DATA, RESULTING A FINAL R VALUE OF 0.166.

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.166	1648	3.32 %	random selection
Rwork	0.166	-	-	-
obs	0.166	49678	98.6 %	-

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / B_sol: 42.37 Ų / k_sol: 0.34 e/ų

Displacement parameters

	Baniso -1	Baniso -2	Baniso -3
1-	-3.8841 Å2	0 Å2	0 Å2
2-	-	-3.8841 Å2	0 Å2
3-	-	-	7.7682 Å2

Refinement step

Cycle: LAST / Resolution: 1.9→59.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3210	0	60	396	3666

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	3363
X-RAY DIFFRACTION	f_angle_d	1.068	4548
X-RAY DIFFRACTION	f_dihedral_angle_d	12.948	1212
X-RAY DIFFRACTION	f_chiral_restr	0.078	493
X-RAY DIFFRACTION	f_plane_restr	0.004	585

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
1.9009-1.9225	0.3176	1446	0.3176	1446	X-RAY DIFFRACTION	89
1.9225-1.9451	0.2848	1537	0.2848	1537	X-RAY DIFFRACTION	92
1.9451-1.9688	0.2534	1529	0.2534	1529	X-RAY DIFFRACTION	93
1.9688-1.9937	0.2352	1536	0.2352	1536	X-RAY DIFFRACTION	94
1.9937-2.02	0.234	1580	0.234	1580	X-RAY DIFFRACTION	96
2.02-2.0476	0.2142	1605	0.2142	1605	X-RAY DIFFRACTION	97
2.0476-2.0769	0.2103	1622	0.2103	1622	X-RAY DIFFRACTION	98
2.0769-2.1079	0.184	1637	0.184	1637	X-RAY DIFFRACTION	100
2.1079-2.1408	0.1746	1663	0.1746	1663	X-RAY DIFFRACTION	100
2.1408-2.1759	0.1629	1665	0.1629	1665	X-RAY DIFFRACTION	100
2.1759-2.2135	0.162	1661	0.162	1661	X-RAY DIFFRACTION	100
2.2135-2.2537	0.1546	1651	0.1546	1651	X-RAY DIFFRACTION	100
2.2537-2.2971	0.1584	1645	0.1584	1645	X-RAY DIFFRACTION	100
2.2971-2.344	0.1454	1680	0.1454	1680	X-RAY DIFFRACTION	100
2.344-2.3949	0.1494	1662	0.1494	1662	X-RAY DIFFRACTION	100
2.3949-2.4506	0.1538	1673	0.1538	1673	X-RAY DIFFRACTION	100
2.4506-2.5119	0.1566	1661	0.1566	1661	X-RAY DIFFRACTION	100
2.5119-2.5798	0.1564	1678	0.1564	1678	X-RAY DIFFRACTION	100
2.5798-2.6557	0.158	1658	0.158	1658	X-RAY DIFFRACTION	100
2.6557-2.7415	0.162	1679	0.162	1679	X-RAY DIFFRACTION	100
2.7415-2.8394	0.169	1677	0.169	1677	X-RAY DIFFRACTION	100
2.8394-2.9531	0.1675	1672	0.1675	1672	X-RAY DIFFRACTION	100
2.9531-3.0875	0.1705	1686	0.1705	1686	X-RAY DIFFRACTION	100
3.0875-3.2503	0.1707	1697	0.1707	1697	X-RAY DIFFRACTION	100
3.2503-3.4539	0.1551	1690	0.1551	1690	X-RAY DIFFRACTION	100
3.4539-3.7206	0.145	1713	0.145	1713	X-RAY DIFFRACTION	100
3.7206-4.0949	0.1276	1703	0.1276	1703	X-RAY DIFFRACTION	100
4.0949-4.6872	0.1326	1739	0.1326	1739	X-RAY DIFFRACTION	100
4.6872-5.9045	0.1484	1755	0.1484	1755	X-RAY DIFFRACTION	100
5.9045-59.0945	0.1908	1878	0.1908	1878	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	0.8444	-0.0179	-0.3245	0.8859	-0.553	0.4729	0.0151	0.1074	-0.0472	-0.083	-0.0461	-0.0807	0.1154	-0.0631	0.0313	0.1966	0.0266	-0.0015	0.1981	-0.0464	0.2138	27.6263	50.8891	24.6808
2	0.8402	-0.7536	-0.8428	1.6493	0.2253	1.5715	0.1715	0.2617	0.1618	-0.3399	0.0363	-0.8614	-0.0329	0.2939	-0.006	0.257	0.0351	0.0343	0.3309	-0.0077	0.2938	35.4201	54.5246	16.9509
3	0.72	-0.0826	-0.1504	0.692	-0.3066	0.5063	0.0626	0.2064	-0.0441	-0.2339	-0.0791	-0.0076	-0.0277	-0.0536	0.0223	0.2672	0.0236	-0.0265	0.2459	-0.0382	0.1878	18.4553	57.656	15.258
4	0.4664	-0.3316	0.133	0.7308	0.2993	0.7666	-0.0036	-0.0553	-0.2209	0.0367	0.0134	0.0247	0.074	0.0122	0.0005	0.1456	-0.0049	-0.003	0.1701	-0.016	0.2277	17.1135	47.4951	32.4944
5	0.174	0.0832	-0.0265	0.4803	0.263	0.1696	-0.051	-0.1377	-0.1145	0.0834	0.0394	0.2239	0.0758	0.0481	0.0053	0.156	-0.0063	-0.007	0.1828	-0.0046	0.2647	9.4197	50.1399	44.0168
6	0.4067	0.1889	0.3751	0.0933	0.1853	0.3229	-0.018	-0.1345	-0.0318	0.0581	0.0394	-0.1105	-0.0435	0.1034	-0.0114	0.1578	0.0303	0.0087	0.1918	0.0048	0.2033	20.1776	60.6329	61.3002
7	0.2537	-0.1292	-0.1738	0.1142	0.0887	0.0978	0.0103	0.0325	-0.0414	-0.0997	-0.0065	-0.0713	-0.0473	0.0141	0.0094	0.1466	0.0059	0.008	0.1573	-0.0091	0.157	18.4485	67.0087	53.1592
8	0.1894	-0.2472	-0.046	0.368	0.1331	0.128	-0.0769	0.0453	-0.0954	-0.0871	0.0212	0.2326	0.0047	-0.1739	0.05	0.1614	0.0059	-0.0084	0.2177	0.006	0.2839	10.0189	64.5223	46.0245
9	0.2946	0.084	0.0697	0.1063	0.2373	0.5677	-0.0249	-0.0867	0.0766	-0.0232	-0.0571	0.0529	-0.0143	-0.18	0.0728	0.1533	0.021	-0.0047	0.1836	-0.0091	0.2079	12.2146	73.0002	60.26
10	0.5298	0.4186	0.0579	0.9737	0.0522	0.4836	0.01	-0.4433	0.1399	0.288	-0.1888	0.1857	0.0355	-0.1407	0.1358	0.2038	-0.0054	0.0366	0.2465	0.0046	0.2209	11.2783	60.6398	69.4125
11	0.8631	-0.0944	-0.1547	0.0358	-0.0379	0.2768	0.0432	-0.1159	-0.246	-0.0735	-0.0855	-0.1311	-0.0209	0.0589	0.0372	0.2001	0.0125	0.0385	0.1604	-0.0137	0.3146	23.7942	78.3751	64.5592

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 2:51)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 52:68)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 69:164)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 165:239)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 240:253)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 254:295)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 296:327)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 328:339)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 340:375)
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 376:400)
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 484:484)