PDB-2ohi: Crystal Structure of coenzyme F420H2 oxidase (FprA), a diiron fla...

ID or keywords:

Entry

Database: PDB / ID: 2ohi

Title

Crystal Structure of coenzyme F420H2 oxidase (FprA), a diiron flavoprotein, reduced state

Components

Type A flavoprotein fprA

Keywords

OXIDOREDUCTASE / beta-lactamase like domain / flavodoxine like domain

Function / homology

Function and homology information

coenzyme F420H2 oxidase / FMN binding / oxidoreductase activity / electron transfer activity / metal ion binding
Similarity search - Function

Biological species

Methanothermobacter thermautotrophicus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Seedorf, H. / Warkentin, E. / Ermler, U.

Citation

Journal: Febs J. / Year: 2007
Title: Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic Archaea catalyzing the reduction of O2 to H2O.
Authors: Seedorf, H. / Hagemeier, C.H. / Shima, S. / Thauer, R.K. / Warkentin, E. / Ermler, U.

History

Deposition	Jan 10, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 22, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Dec 27, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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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PDBx/mmCIF format	2ohi.cif.gz	624.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2ohi_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	2ohi_full_validation.pdf.gz	3.1 MB	Display
Data in XML	2ohi_validation.xml.gz	117 KB	Display
Data in CIF	2ohi_validation.cif.gz	157.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oh/2ohi ftp://data.pdbj.org/pub/pdb/validation_reports/oh/2ohi	HTTPS FTP

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Related structure data

Related structure data	2ohhC 2ohjC C: citing same article (ref.)
Similar structure data	2ohj-1 2ohj-2 2ohh-1 1ycf-1 1ycg-2 3q8f-d 2ohh-2 1ycf-2 4gl4-1 5kms-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

2ohhC

2ohjC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #133 - Jan 2011 Nitric Oxide Synthase similarity (3) #228 - Dec 2018 Directed Evolution of Enzymes similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Type A flavoprotein fprA

B: Type A flavoprotein fprA

D: Type A flavoprotein fprA

E: Type A flavoprotein fprA

G: Type A flavoprotein fprA

H: Type A flavoprotein fprA

I: Type A flavoprotein fprA

J: Type A flavoprotein fprA

hetero molecules

367 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Type A flavoprotein fprA

B: Type A flavoprotein fprA

hetero molecules

defined by author&software
91.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Type A flavoprotein fprA

E: Type A flavoprotein fprA

hetero molecules

defined by author&software
91.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Type A flavoprotein fprA

H: Type A flavoprotein fprA

hetero molecules

defined by author&software
91.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

I: Type A flavoprotein fprA

J: Type A flavoprotein fprA

hetero molecules

defined by author&software
91.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

G: Type A flavoprotein fprA

H: Type A flavoprotein fprA

I: Type A flavoprotein fprA

J: Type A flavoprotein fprA

hetero molecules

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

6

A: Type A flavoprotein fprA

B: Type A flavoprotein fprA

D: Type A flavoprotein fprA

E: Type A flavoprotein fprA

hetero molecules

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

Unit cell

Length a, b, c (Å)	97.798, 123.113, 135.864
Angle α, β, γ (deg.)	90.00, 103.40, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	J
2	1	A
3	1	B
4	1	D
5	1	E
6	1	G
7	1	H
8	1	I

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 5 / Auth seq-ID: 2 - 402 / Label seq-ID: 2 - 402

Dom-ID	Auth asym-ID	Label asym-ID
1	J	H
2	A	A
3	B	B
4	D	C
5	E	D
6	G	E
7	H	F
8	I	G

#1: Protein	Type A flavoprotein fprA / FMN-protein fprA / Flavoprotein A Mass: 45255.582 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Strain: DSZM2133 / Gene: fprA, fpaA / Production host: Escherichia coli (E. coli) / References: UniProt: Q50497, Oxidoreductases
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.01 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.001M DDT, 0.2M ammonium sulfate, 0.1M MES/KOH, 30% PEG MME 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2006 / Details: mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→20 Å / Num. all: 103861 / Num. obs: 103861 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / R_sym value: 6.6 / Net I/σ(I): 13.7
Reflection shell	Resolution: 2.3→2.35 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.8 / R_sym value: 36.4 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data collection
XDS		data reduction
XDS		data scaling
EPMR		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.909 / SU B: 19.899 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26907	5530	5.1 %	RANDOM
R_work	0.20281	-	-	-
obs	0.2061	103861	78.87 %	-
all	-	103861	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 43.975 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.85 Å²	0 Å²	-1.61 Å²
2-	-	-1.39 Å²	0 Å²
3-	-	-	-1.21 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25296	0	268	365	25929

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	26145
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.363	1.981	35475
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.908	5	3216
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.345	24.015	1183
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.759	15	4432
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.62	15	160
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	3919
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	19732
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	12490
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	17441
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	1198
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.037	0.2	1
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.217	0.2	66
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.141	0.2	14
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.457	1.5	16406
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.811	2	25654
X-RAY DIFFRACTION	r_scbond_it	1.221	3	11389
X-RAY DIFFRACTION	r_scangle_it	1.914	4.5	9821
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	J	1604	medium positional	0.26	0.5
2	A	1604	medium positional	0.2	0.5
3	B	1604	medium positional	0.24	0.5
4	D	1604	medium positional	0.22	0.5
5	E	1604	medium positional	0.23	0.5
6	G	1604	medium positional	0.24	0.5
7	H	1604	medium positional	0.27	0.5
8	I	1604	medium positional	0.22	0.5
1	J	1522	loose positional	0.5	5
2	A	1522	loose positional	0.55	5
3	B	1522	loose positional	0.57	5
4	D	1522	loose positional	0.51	5
5	E	1522	loose positional	0.54	5
6	G	1522	loose positional	0.53	5
7	H	1522	loose positional	0.66	5
8	I	1522	loose positional	0.52	5
1	J	1604	medium thermal	0.48	2
2	A	1604	medium thermal	0.38	2
3	B	1604	medium thermal	0.45	2
4	D	1604	medium thermal	0.47	2
5	E	1604	medium thermal	0.36	2
6	G	1604	medium thermal	0.43	2
7	H	1604	medium thermal	0.43	2
8	I	1604	medium thermal	0.35	2
1	J	1522	loose thermal	1.54	10
2	A	1522	loose thermal	1.27	10
3	B	1522	loose thermal	1.4	10
4	D	1522	loose thermal	1.39	10
5	E	1522	loose thermal	1.16	10
6	G	1522	loose thermal	1.41	10
7	H	1522	loose thermal	1.27	10
8	I	1522	loose thermal	1.2	10

LS refinement shell

Resolution: 2.3→2.359 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.342	385	-
R_work	0.245	6150	-
obs	-	-	64.44 %

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	2.1342	0.0746	-0.3389	2.4557	0.4251	1.9344	0.017	0.1155	-0.3458	-0.0568	0.2182	-0.7453	0.1805	0.546	-0.2352	-0.1068	0.1131	-0.0725	0.1222	-0.1976	0.2433	109.463	33.522	134.383
2	2.7102	-1.0841	0.0541	1.8149	0.3502	3.0329	-0.0377	-0.0936	-0.1354	0.1856	0.1311	-0.0076	0.2256	-0.1027	-0.0935	-0.1235	-0.0135	0.0087	-0.233	0.0129	-0.1518	72.749	36.227	140.6
3	2.1053	-1.0422	-0.1492	1.9253	0.6516	2.3827	-0.1433	-0.2418	-0.0951	0.0728	0.1356	0.2996	-0.1627	-0.3315	0.0077	-0.1116	-0.0064	-0.0123	-0.0964	0.0589	-0.115	51.508	52.109	116.509
4	3.0266	0.0397	0.3679	1.3886	0.2305	2.0863	-0.0353	0.1131	-0.0769	-0.1178	0.1456	-0.2437	0.0091	0.2577	-0.1102	-0.1591	-0.0519	0.0458	-0.2137	-0.0637	-0.1115	81.573	30.272	112.111
5	2.644	-1.1049	-0.0666	2.0947	0.2769	1.1862	-0.1264	-0.1108	0.0464	0.1836	0.1584	0.0464	-0.016	0.0507	-0.032	-0.0732	0.0384	-0.0461	-0.1883	-0.001	-0.1868	74.635	66.242	152.229
6	2.3137	-0.5847	-0.5239	1.847	0.7147	3.8119	-0.1784	0.1581	0.0208	-0.1779	0.2183	-0.4628	-0.2324	0.4292	-0.0399	-0.0898	-0.1796	0.0414	-0.0503	-0.0648	0.0956	103.126	64.673	128.136
7	2.6985	-0.2697	-0.0847	3.6845	0.2368	1.6306	-0.1114	0.2554	-0.0792	-0.7177	0.3155	-0.8197	-0.2369	0.4854	-0.2041	0.1338	-0.2618	0.2847	0.1346	-0.1369	0.0574	97.625	52.38	94.852
8	1.9492	-0.7481	-0.5139	1.4853	0.8612	2.7492	-0.1376	0.1029	0.1961	-0.2876	0.0752	-0.1063	-0.4864	0.0992	0.0623	0.1166	-0.0959	-0.0168	-0.192	0.0229	-0.1272	75.984	73.046	117.104
9	1.6516	-0.5997	-0.0049	2.2622	0.302	2.3385	-0.1797	-0.224	0.0301	0.0273	0.1261	0.4213	-0.2574	-0.3491	0.0536	-0.0219	0.0701	-0.072	-0.0811	0.0329	-0.0646	19.131	50.469	49.912
10	2.6165	0.1571	0.2563	1.1461	0.4571	2.3307	-0.0303	0.1059	-0.0347	-0.1366	0.152	-0.2332	0.039	0.1865	-0.1217	-0.1138	-0.0577	0.0397	-0.2248	-0.0622	-0.1188	48.736	27.967	46.432
11	2.5981	0.2183	0.0965	2.08	0.9031	2.4422	-0.0069	0.2368	-0.4451	-0.0475	0.3284	-0.5835	0.2196	0.5824	-0.3216	-0.0899	0.1074	-0.0331	0.0221	-0.1783	0.1174	76.367	31.135	69.141
12	3.0522	-0.6203	0.2064	1.9004	0.3069	2.3421	-0.0007	-0.074	-0.1553	0.0816	0.0512	0.0539	0.1456	-0.1694	-0.0504	-0.1215	-0.0107	0.0269	-0.2352	0.007	-0.1665	39.581	34.404	74.648
13	3.0812	-1.1558	-0.3451	2.1216	0.484	2.0709	-0.1266	0.3856	0.0112	-0.3174	0.1568	-0.3491	-0.2523	0.4891	-0.0302	0.1257	-0.3099	0.0884	0.2245	-0.0167	-0.1257	65.57	49.462	29.156
14	2.4261	-0.6273	-0.1396	0.9328	0.287	2.7208	-0.2249	0.1564	0.2919	-0.3491	0.0934	0.0489	-0.6057	0.1485	0.1315	0.263	-0.104	-0.1149	-0.1595	0.0376	-0.1015	43.939	70.966	50.782
15	2.3336	-0.8795	-0.0832	1.6318	0.3968	1.3542	-0.0919	-0.0704	0.0682	-0.0494	0.0847	0.0962	-0.1488	-0.0062	0.0071	-0.1437	0.0324	-0.0153	-0.2044	-0.0195	-0.1728	41.713	64.368	85.964
16	2.1951	-0.4918	-0.5492	1.655	0.768	3.7392	-0.2207	0.1808	0.1177	-0.2993	0.264	-0.2139	-0.5166	0.5489	-0.0433	-0.0073	-0.2029	0.0397	-0.0457	-0.0449	-0.0763	70.672	62.283	62.295

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 - 250	1 - 250
2	X-RAY DIFFRACTION	2	A	A	251 - 403	251 - 403
3	X-RAY DIFFRACTION	3	B	B	1 - 250	1 - 250
4	X-RAY DIFFRACTION	4	B	B	251 - 403	251 - 403
5	X-RAY DIFFRACTION	5	D	C	1 - 250	1 - 250
6	X-RAY DIFFRACTION	6	D	C	251 - 403	251 - 403
7	X-RAY DIFFRACTION	7	E	D	1 - 250	1 - 250
8	X-RAY DIFFRACTION	8	E	D	251 - 403	251 - 403
9	X-RAY DIFFRACTION	9	G	E	1 - 250	1 - 250
10	X-RAY DIFFRACTION	10	G	E	251 - 403	251 - 403
11	X-RAY DIFFRACTION	11	H	F	1 - 250	1 - 250
12	X-RAY DIFFRACTION	12	H	F	251 - 403	251 - 403
13	X-RAY DIFFRACTION	13	I	G	1 - 250	1 - 250
14	X-RAY DIFFRACTION	14	I	G	251 - 403	251 - 403
15	X-RAY DIFFRACTION	15	J	H	1 - 250	1 - 250
16	X-RAY DIFFRACTION	16	J	H	251 - 403	251 - 403

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