PDB-5lld: Flavodiiron core of Escherichia coli flavorubredoxin in the reduc...

Basic information

• Entry: Database: PDB / ID: 5lld
• Title: Flavodiiron core of Escherichia coli flavorubredoxin in the reduced form.
• 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:

: / FLAVIN MONONUCLEOTIDE / OXYGEN MOLECULE / Anaerobic nitric oxide reductase flavorubredoxin

• Biological species: Escherichia coli (E. coli)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.651 Å
• Authors: Romao, C.V. / Borges, P.T. / Vicente, J.B. / Carrondo, M.A. / Teixeira, M. / Frazao, C.

Funding support

Portugal, 2items

Organization	Grant number	Country
FCT	PTDC/BBB-BQB/3135/2014	Portugal
FEDER	LISBOA-01-0145-FEDER-007660	Portugal

• 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 27, 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: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Assembly

Deposited unit

A: Anaerobic nitric oxide reductase flavorubredoxin

hetero molecules

Summary:

• 54.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	54,893	5
Polymers	54,293	1
Non-polymers	600	4
Water	2,306	128

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
• 220 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	219,572	20
Polymers	217,172	4
Non-polymers	2,400	16
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

Unit cell

Length a, b, c (Å)	151.700, 151.700, 96.500
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	177
Space group name H-M	P622

Components

#1: Protein

A Anaerobic nitric oxide reductase flavorubredoxin / FlavoRb

Details:

Mass: 54293.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: norV, flrD, ygaI, ygaJ, ygaK, b2710, JW2680 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46877

#2: Chemical

A-501 A-502 ChemComp-FE / FE (III) ION

Details:

Mass: 55.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe

#3: Chemical

A-503 ChemComp-OXY / OXYGEN MOLECULE

Details:

Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O₂

#4: Chemical

A-504 ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE

Details:

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

#5: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.95 ų/Da / Density % sol: 58.33 %
• Crystal grow: Temperature: 304 K / Method: vapor diffusion, hanging drop / pH: 6.5 ; Details: 1.0UL OF PROTEIN AT15 MG/ML WITH 0.8UL OF CRYSTALLIZATION SOLUTION (0.2M NA-CACODYLATE PH 6.5, 0.2 M MGACETATE, 20% PEG8000) and 0.2UL OF 0.1M HEXAMINE COBALT (III).

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
• Detector: Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2008
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.8726 Å / Relative weight: 1
• Reflection: Resolution: 2.65→45.34 Å / Num. obs: 17773 / % possible obs: 91 % / Redundancy: 6.3 % / B_iso Wilson estimate: 18 Ų / R_sym value: 0.157 / Net I/σ(I): 5.9
• Reflection shell: Resolution: 2.65→2.74 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.5 / CC_1/2: 0.8 / % possible all: 90.3

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: 2.651→45.292 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.35 / Phase error: 13.9 / Stereochemistry target values: ML
Details: The final model was refined versus the full data, resulting in R value of 0.19. The rubredoxin domain in C-terminal was not visible since it is disordered.

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.246	17132	10 %	random
Rwork	0.185	-	-	-
obs	0.1899	1713	87.72 %	-

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 0.438 Ų / k_sol: 0.297 e/ų

Displacement parameters

	Baniso -1	Baniso -2	Baniso -3
1-	-9.168 Å2	0 Å2	-0 Å2
2-	-	-9.168 Å2	-0 Å2
3-	-	-	-2.4335 Å2

Refinement step

Cycle: LAST / Resolution: 2.651→45.292 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3200	0	35	128	3363

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	3318
X-RAY DIFFRACTION	f_angle_d	0.566	4494
X-RAY DIFFRACTION	f_dihedral_angle_d	10.846	1198
X-RAY DIFFRACTION	f_chiral_restr	0.044	489
X-RAY DIFFRACTION	f_plane_restr	0.002	581

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
2.6512-2.6813	0.241	495	0.241	495	X-RAY DIFFRACTION	77
2.6813-2.7128	0.2263	511	0.2263	511	X-RAY DIFFRACTION	81
2.7128-2.7459	0.242	532	0.242	532	X-RAY DIFFRACTION	84
2.7459-2.7807	0.2198	531	0.2198	531	X-RAY DIFFRACTION	85
2.7807-2.8173	0.2013	568	0.2013	568	X-RAY DIFFRACTION	87
2.8173-2.8559	0.22	557	0.22	557	X-RAY DIFFRACTION	87
2.8559-2.8966	0.2145	547	0.2145	547	X-RAY DIFFRACTION	88
2.8966-2.9399	0.2018	565	0.2018	565	X-RAY DIFFRACTION	88
2.9399-2.9858	0.2155	564	0.2155	564	X-RAY DIFFRACTION	88
2.9858-3.0347	0.2005	569	0.2005	569	X-RAY DIFFRACTION	89
3.0347-3.0871	0.2041	568	0.2041	568	X-RAY DIFFRACTION	90
3.0871-3.1432	0.1843	586	0.1843	586	X-RAY DIFFRACTION	91
3.1432-3.2036	0.1709	571	0.1709	571	X-RAY DIFFRACTION	89
3.2036-3.269	0.1876	567	0.1876	567	X-RAY DIFFRACTION	89
3.269-3.3401	0.1837	586	0.1837	586	X-RAY DIFFRACTION	91
3.3401-3.4177	0.1653	566	0.1653	566	X-RAY DIFFRACTION	89
3.4177-3.5032	0.1606	584	0.1606	584	X-RAY DIFFRACTION	90
3.5032-3.5978	0.1376	580	0.1376	580	X-RAY DIFFRACTION	89
3.5978-3.7037	0.1406	584	0.1406	584	X-RAY DIFFRACTION	90
3.7037-3.8232	0.1345	580	0.1345	580	X-RAY DIFFRACTION	90
3.8232-3.9597	0.1304	581	0.1304	581	X-RAY DIFFRACTION	90
3.9597-4.1182	0.1312	579	0.1312	579	X-RAY DIFFRACTION	88
4.1182-4.3055	0.1281	580	0.1281	580	X-RAY DIFFRACTION	88
4.3055-4.5322	0.1343	586	0.1343	586	X-RAY DIFFRACTION	90
4.5322-4.8159	0.134	584	0.134	584	X-RAY DIFFRACTION	88
4.8159-5.1873	0.1381	581	0.1381	581	X-RAY DIFFRACTION	88
5.1873-5.7084	0.1724	596	0.1724	596	X-RAY DIFFRACTION	89
5.7084-6.5323	0.2046	584	0.2046	584	X-RAY DIFFRACTION	87
6.5323-8.2219	0.2002	608	0.2002	608	X-RAY DIFFRACTION	88
8.2219-45.2986	0.2204	642	0.2204	642	X-RAY DIFFRACTION	84

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	0.1942	-0.2973	0.2538	0.6214	-0.2043	0.4821	-0.1148	0.2491	0.0144	0.1074	0.0256	-0.1024	0.0384	0.1511	-0.1618	0.0684	-0.0187	0.0267	0.1757	-0.0859	0.1055	28.0007	51.3368	25.5338
2	0.0554	0.0022	0.0365	0.04	0.0365	0.0586	0.004	-0.0516	0.0569	-0.003	-0.0487	-0.0405	0.021	0.0012	-0.0166	0.0719	0.129	0.0466	0.2918	0.0079	0.2888	34.8428	55.8163	19.0509
3	0.2057	-0.0306	0.1825	0.247	-0.2334	0.3857	0.0948	0.1215	0.0615	-0.1446	-0.1805	0.0701	0.109	-0.0018	-0.1149	0.1409	-0.0629	0.0613	0.2168	-0.1044	0.0758	26.0675	57.9136	15.6273
4	0.091	0.0483	-0.0268	0.2008	-0.1095	0.2637	-0.0863	0.1339	-0.1836	0.03	-0.0176	-0.0716	0.022	-0.1365	-0.0122	0.0556	-0.0272	0.0214	0.163	-0.0415	0.1134	18.9127	55.2256	19.7111
5	0.007	0.0022	0.0039	0.0096	0.0044	0.0042	-0.0522	0.0543	-0.0187	0.0776	-0.1167	-0.1185	-0.0139	-0.0295	-0	0.0867	-0.0973	0.0306	0.3529	-0.0596	0.2905	21.8504	50.018	40.9945
6	0.7048	-0.5763	0.1352	0.4878	-0.1305	0.5872	0.0169	-0.1058	-0.2869	-0.0627	0.1536	0.2141	-0.0861	0.1106	0.0448	0.019	-0.0437	0.0039	0.1694	0.0133	0.0921	11.7328	49.1269	31.9176
7	0.2119	0.12	-0.1062	0.2707	0.0824	0.3145	-0.0853	-0.0418	0.0916	0.0308	0.0382	0.1571	0.0514	-0.0672	-0.0342	0.0144	0.0404	-0.0052	0.0548	0.0148	0.0244	15.2167	65.0405	59.4495
8	0.0014	0.008	0.0106	0.0498	0.0636	0.0808	-0.0315	-0.0409	0.0634	-0.0198	-0.0278	-0.0261	0.0088	-0.0021	-0.062	0.0187	0.0302	-0.042	0.0274	-0.0809	0.2254	23.9294	78.9073	65.1987

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 3:48)
2	X-RAY DIFFRACTION	2	(chain A and resid 49:66)
3	X-RAY DIFFRACTION	3	(chain A and resid 67:90)
4	X-RAY DIFFRACTION	4	(chain A and resid 91:185)
5	X-RAY DIFFRACTION	5	(chain A and resid 186:194)
6	X-RAY DIFFRACTION	6	(chain A and resid 195:246)
7	X-RAY DIFFRACTION	7	(chain A and resid 247:400)
8	X-RAY DIFFRACTION	8	(chain A and resid 601:601)