PDB-8g64: Heme-bound flavodoxin FldH from Fusobacterium nucleatum

ID or keywords:

Entry

Database: PDB / ID: 8g64

Title

Heme-bound flavodoxin FldH from Fusobacterium nucleatum

Components

Flavodoxin

Keywords

FLAVOPROTEIN / anaerobilin / FMN-containing flavodoxin / heme acquisition chaperone / HmuF homolog

Function / homology

Function and homology information

FMN binding / metal ion binding
Similarity search - Function

Biological species

Fusobacterium nucleatum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Chan, A.C. / Wolthers, K.R. / Murphy, M.E.

Funding support

Canada, 1items

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: A new member of the flavodoxin superfamily from Fusobacterium nucleatum that functions in heme trafficking and reduction of anaerobilin.
Authors: McGregor, A.K. / Chan, A.C.K. / Schroeder, M.D. / Do, L.T.M. / Saini, G. / Murphy, M.E.P. / Wolthers, K.R.

History

Deposition	Feb 14, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 9, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8g64.cif.gz	125.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8g64.ent.gz	96.8 KB	Display	PDB format
PDBx/mmJSON format	8g64.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g6/8g64 ftp://data.pdbj.org/pub/pdb/validation_reports/g6/8g64	HTTPS FTP

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Related structure data

Similar structure data	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 (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Flavodoxin

hetero molecules

20.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	67.240, 67.240, 99.650
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-511- HOH

#1: Protein	Flavodoxin Mass: 19599.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Gene: FN1822 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q8RI14
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.32 Å³/Da / Density % sol: 62.93 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M sodium citrate pH 5.5, 2 M ammonium sulphate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08B1-1 / Wavelength: 0.99184 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.99184 Å / Relative weight: 1

Reflection

Resolution: 1.6→37.86 Å / Num. obs: 66287 / % possible obs: 99.6 % / Redundancy: 9.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.063 / R_rim(I) all: 0.067 / Net I/σ(I): 18.49

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.6-1.7	0.787	5678	0.843	0.83	1
1.7-1.82	0.486	5324	0.94	0.511	1
1.82-1.96	0.264	4644	0.981	0.278	1
1.96-2.11	0.151	3740	0.992	0.16	1
2.11-2.3	0.103	3440	0.996	0.109	1
2.3-2.53	0.081	2942	0.997	0.085	1
2.53-2.8	0.064	2341	0.998	0.067	1
2.8-3.15	0.051	1964	0.999	0.054	1
3.15-3.59	0.043	1507	0.998	0.046	1
3.59-4.18	0.04	1181	0.999	0.042	1
4.18-5	0.039	850	0.999	0.041	1
5-10	0.038	1265	0.999	0.04	1

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1	refinement
XSCALE		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→37.86 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1783	3341	5.04 %
R_work	0.1596	-	-
obs	0.1605	66287	99.66 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→37.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1352	0	79	259	1690

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	1489
X-RAY DIFFRACTION	f_angle_d	0.862	2026
X-RAY DIFFRACTION	f_dihedral_angle_d	17.29	193
X-RAY DIFFRACTION	f_chiral_restr	0.054	216
X-RAY DIFFRACTION	f_plane_restr	0.006	249

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 (%)
1.6-1.62	0.2567	139	0.2481	2586	X-RAY DIFFRACTION	99
1.62-1.65	0.2359	138	0.2331	2675	X-RAY DIFFRACTION	99
1.65-1.67	0.2627	134	0.228	2572	X-RAY DIFFRACTION	99
1.67-1.7	0.307	137	0.2443	2579	X-RAY DIFFRACTION	99
1.7-1.73	0.2753	141	0.2338	2654	X-RAY DIFFRACTION	99
1.73-1.76	0.2125	138	0.231	2640	X-RAY DIFFRACTION	99
1.76-1.79	0.2372	136	0.204	2581	X-RAY DIFFRACTION	99
1.79-1.83	0.1884	135	0.185	2588	X-RAY DIFFRACTION	99
1.83-1.87	0.2218	142	0.1713	2673	X-RAY DIFFRACTION	100
1.87-1.91	0.1558	138	0.1651	2623	X-RAY DIFFRACTION	99
1.91-1.96	0.1858	139	0.1627	2612	X-RAY DIFFRACTION	100
1.96-2.02	0.1691	137	0.1613	2608	X-RAY DIFFRACTION	100
2.02-2.08	0.1948	140	0.1735	2644	X-RAY DIFFRACTION	100
2.08-2.14	0.1874	137	0.1588	2609	X-RAY DIFFRACTION	100
2.14-2.22	0.1533	144	0.1436	2628	X-RAY DIFFRACTION	100
2.22-2.31	0.1482	142	0.1348	2648	X-RAY DIFFRACTION	100
2.31-2.41	0.1685	141	0.1472	2615	X-RAY DIFFRACTION	100
2.41-2.54	0.15	138	0.1475	2626	X-RAY DIFFRACTION	100
2.54-2.7	0.18	144	0.1482	2659	X-RAY DIFFRACTION	100
2.7-2.91	0.1974	135	0.1527	2600	X-RAY DIFFRACTION	100
2.91-3.2	0.1866	141	0.1551	2643	X-RAY DIFFRACTION	100
3.2-3.66	0.1707	139	0.1462	2612	X-RAY DIFFRACTION	100
3.66-4.61	0.1392	144	0.1299	2639	X-RAY DIFFRACTION	100
4.61-37.86	0.1882	142	0.181	2632	X-RAY DIFFRACTION	100

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	0.6177	-0.5197	-0.528	1.542	0.4037	0.4012	-0.1309	-0.1781	0.2412	-0.0377	-0.0017	-0.0247	-0.0982	0.0049	-0.0008	0.2295	0.0331	-0.0232	0.2138	0.0104	0.252	14.0067	49.1827	31.5862
2	0.3048	0.3177	-0.141	0.5576	-0.4356	0.3594	0.0763	-0.3377	0.5368	0.0759	-0.1709	0.3313	-0.1923	-0.203	0.0069	0.2428	0.0146	0.02	0.2393	-0.0889	0.2667	8.587	49.5625	38.1075
3	0.3133	0.1563	-0.2193	1.4254	0.186	0.1989	-0.0568	0.0174	0.1407	-0.1283	-0.0408	-0.3596	-0.1474	0.0667	0.0003	0.2892	0.0216	-0.0145	0.2016	0.0054	0.2525	17.5413	53.9199	30.5855
4	0.5238	-0.3657	-0.4539	1.3038	-0.4952	0.7929	-0.0984	0.0698	-0.1735	-0.2043	0.0231	-0.4886	-0.0473	0.0529	-0.0047	0.2382	0.0154	0.025	0.1923	-0.0076	0.2782	21.106	48.081	30.4484
5	0.2857	0.1033	-0.1715	0.141	-0.3207	0.5889	-0.0644	0.3654	-0.2125	-0.3636	-0.0424	0.0151	0.0286	-0.0982	0	0.2808	0.0319	0.0196	0.2338	-0.0303	0.1907	12.8755	39.5667	22.5385
6	0.646	-0.3939	0.7692	1.7144	0.1292	1.0677	0.1107	0.0227	-0.04	-0.0334	-0.1077	-0.0608	0.1129	-0.0389	0.0004	0.2097	0.0304	-0.0072	0.1626	-0.0076	0.1718	14.0324	37.9126	33.149
7	0.7117	-0.087	0.6652	0.0814	-0.1736	0.6188	0.0023	0.0225	-0.5505	-0.2882	-0.0822	-0.129	0.2919	0.0466	0.001	0.2845	0.0297	0.0319	0.1999	-0.0298	0.303	14.4945	30.9414	29.7206
8	0.4513	0.4879	0.4003	1.0016	0.3268	0.3685	0.1948	-0.03	0.0371	-0.0597	-0.1714	-0.0896	0.1585	0.0156	0.0416	0.2189	0.0354	0.0093	0.2102	0.0201	0.2015	15.4462	37.0914	35.353
9	0.4601	0.0652	-0.3324	0.0323	0.063	0.3659	-0.2205	0.0542	0.1861	-0.2372	0.0126	0.1175	-0.4589	-0.4657	-0.0003	0.3181	0.0488	-0.078	0.3075	-0.0501	0.2981	-7.2555	39.9451	24.6666
10	0.1744	0.0217	-0.1576	0.1966	-0.1577	0.2353	0.1294	-0.0204	0.1105	-0.2849	-0.2635	0.2558	0.0416	-0.5742	-0.0143	0.304	-0.0262	-0.04	0.3686	-0.0399	0.2649	-8.0481	30.9558	17.047
11	1.1241	0.7094	-0.6712	0.8801	-0.7827	0.7037	-0.1557	0.0394	0.0431	-0.004	0.1139	0.3105	0.1931	-0.2371	0.0022	0.2257	-0.0361	-0.0083	0.2885	-0.0323	0.2822	-6.4937	32.8645	32.3018
12	0.4781	-0.0715	-0.2039	0.2902	-0.0921	1.0283	0.1506	-0.6672	0.0243	0.1977	-0.1282	-0.0641	0.1511	0.0445	-0.0004	0.2469	-0.0092	-0.0065	0.3155	-0.0624	0.206	12.3291	42.882	45.0315

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 12 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 13 through 24 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 25 through 39 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 40 through 53 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 54 through 69 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 70 through 87 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 88 through 104 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 105 through 114 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 115 through 126 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 127 through 133 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 134 through 152 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 153 through 169 )

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