PDB-7f39: The structure of flavin transferase FmnB

ID or keywords:

Entry

Database: PDB / ID: 7f39

Title

The structure of flavin transferase FmnB

Components

FAD:protein FMN transferase

Keywords

TRANSFERASE / FMN transferase

Function / homology

Function and homology information

FAD:protein FMN transferase / transferase activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Listeria monocytogenes serotype 1/2a

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.888 Å

Authors

Cheng, W. / Zheng, Y.H.

Funding support

1items

Citation

Journal: MedComm (2020) / Year: 2022
Title: Structural insights into the catalytic and inhibitory mechanisms of the flavin transferase FmnB in Listeria monocytogenes.
Authors: Zheng, Y. / Yan, W. / Dou, C. / Zhou, D. / Chen, Y. / Jin, Y. / Yang, L. / Zeng, X. / Cheng, W.

History

Deposition	Jun 15, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 3, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jun 8, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	May 29, 2024	Group: Data collection / Derived calculations / Category: atom_type / chem_comp_atom / chem_comp_bond / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	7f39_validation.pdf.gz	424.8 KB	Display	wwPDB validaton report
Full document	7f39_full_validation.pdf.gz	426.3 KB	Display
Data in XML	7f39_validation.xml.gz	16 KB	Display
Data in CIF	7f39_validation.cif.gz	23.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f3/7f39 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/7f39	HTTPS FTP

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Related structure data

Related structure data	7esaC 7esbC 7escC 7f2uC C: citing same article (ref.)
Similar structure data	7esa-d 7esb-d 7esc-d 1hsk-d 7f2u-2 1vly-d 5aek-1 7f2u-1 4a61-d 5jp6-d 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	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: FAD:protein FMN transferase

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	65.913, 66.768, 87.493
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	FAD:protein FMN transferase / Flavin transferase Mass: 37713.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serotype 1/2a (strain 10403S) (bacteria) Gene: LMRG_02181 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0H3GJF7, FAD:protein FMN transferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

FAD:protein FMN transferase / Flavin transferase

Mass: 37713.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Listeria monocytogenes serotype 1/2a (strain 10403S) (bacteria)
Gene: LMRG_02181
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0H3GJF7, FAD:protein FMN transferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.55 Å³/Da / Density % sol: 51.81 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop Details: 0.2M sodium formate, 20% w/v Polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 1, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 1.888→36.592 Å / Num. obs: 31577 / % possible obs: 99.7 % / Redundancy: 1.1 % / CC_1/2: 1 / R_merge(I) obs: 0.01 / Net I/σ(I): 418.2
Reflection shell	Resolution: 1.89→1.958 Å / Num. unique obs: 3102 / CC_1/2: 1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
PHENIX	1.17	refinement
xia2	0.7.7	data reduction
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.888→36.592 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.934 / SU B: 6.541 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2242	1609	5.095 %
R_work	0.191	29968	-
all	0.193	-	-
obs	-	31577	99.64 %

Solvent computation

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

Displacement parameters

B_iso mean: 29.89 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.727 Å²	0 Å²	-0 Å²
2-	-	-1.447 Å²	0 Å²
3-	-	-	-0.28 Å²

Refinement step

Cycle: LAST / Resolution: 1.888→36.592 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2498	0	0	260	2758

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.013	2542
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2412
X-RAY DIFFRACTION	r_angle_refined_deg	1.869	1.643	3428
X-RAY DIFFRACTION	r_angle_other_deg	1.462	1.594	5607
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.762	5	321
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.8	25.789	114
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.495	15	469
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	27.489	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	339
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2861
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	515
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	497
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	2246
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	1256
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	1249
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	188
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.069	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	14
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.185	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	1.731	2.109	1287
X-RAY DIFFRACTION	r_mcbond_other	1.729	2.108	1286
X-RAY DIFFRACTION	r_mcangle_it	2.578	3.153	1607
X-RAY DIFFRACTION	r_mcangle_other	2.578	3.155	1608
X-RAY DIFFRACTION	r_scbond_it	2.826	2.493	1255
X-RAY DIFFRACTION	r_scbond_other	2.825	2.495	1256
X-RAY DIFFRACTION	r_scangle_it	4.432	3.577	1821
X-RAY DIFFRACTION	r_scangle_other	4.431	3.579	1822
X-RAY DIFFRACTION	r_lrange_it	6.346	41.954	10992
X-RAY DIFFRACTION	r_lrange_other	6.21	41.347	10794

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.888-1.937	0.28	114	0.27	2152	0.271	2294	0.822	0.825	98.7794	0.251
1.937-1.99	0.27	115	0.227	2134	0.229	2253	0.891	0.877	99.8225	0.205
1.99-2.047	0.247	122	0.22	2047	0.221	2171	0.881	0.893	99.9079	0.195
2.047-2.11	0.232	87	0.186	2041	0.188	2130	0.921	0.927	99.9061	0.164
2.11-2.179	0.235	104	0.171	1958	0.174	2062	0.932	0.945	100	0.152
2.179-2.255	0.208	99	0.188	1897	0.189	1996	0.941	0.93	100	0.169
2.255-2.34	0.252	93	0.184	1835	0.187	1929	0.909	0.937	99.9482	0.167
2.34-2.435	0.186	101	0.174	1755	0.175	1860	0.952	0.948	99.7849	0.158
2.435-2.543	0.227	74	0.175	1712	0.177	1793	0.93	0.946	99.6096	0.161
2.543-2.666	0.205	87	0.172	1619	0.174	1706	0.937	0.95	100	0.163
2.666-2.81	0.22	75	0.167	1554	0.169	1630	0.942	0.96	99.9387	0.161
2.81-2.979	0.211	66	0.176	1488	0.177	1554	0.946	0.955	100	0.174
2.979-3.183	0.227	90	0.186	1363	0.189	1458	0.946	0.952	99.6571	0.187
3.183-3.436	0.248	100	0.199	1254	0.203	1370	0.933	0.946	98.8321	0.206
3.436-3.761	0.214	65	0.186	1203	0.187	1269	0.947	0.962	99.9212	0.198
3.761-4.199	0.171	52	0.178	1099	0.178	1151	0.967	0.966	100	0.196
4.199-4.838	0.167	55	0.159	949	0.16	1025	0.973	0.973	97.9512	0.184
4.838-5.9	0.254	43	0.218	843	0.22	888	0.951	0.957	99.7748	0.255
5.9-8.237	0.312	42	0.251	663	0.255	706	0.924	0.934	99.8584	0.29
8.237-36.592	0.27	25	0.247	402	0.249	441	0.938	0.95	96.8254	0.315

Refinement TLS params.

Method: refined / Origin x: 27.3882 Å / Origin y: 16.6269 Å / Origin z: 26.5254 Å

	11	12	13	21	22	23	31	32	33
T	0.0364 Å²	-0.0043 Å²	0.0065 Å²	-	0.0079 Å²	0.0048 Å²	-	-	0.0135 Å²
L	0.956 °²	-0.329 °²	-0.0142 °²	-	1.118 °²	-0.4545 °²	-	-	1.19 °²
S	0.0484 Å °	0.0468 Å °	0.0796 Å °	0.004 Å °	0.0412 Å °	0.0208 Å °	-0.0107 Å °	-0.0045 Å °	-0.0896 Å °

Refinement TLS group

Selection: ALL

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