PDB-4xgx: Crystal structure of Escherichia coli Flavin trafficking protein,...

ID or keywords:

Entry

Database: PDB / ID: 4xgx

Title

Crystal structure of Escherichia coli Flavin trafficking protein, an FMN transferase, Y60N mutant, ADP-inhibited

Components

FAD:protein FMN transferase

Keywords

TRANSFERASE/TRANSFERASE INHIBITOR / flavin transferase / bimetal center / lipoprotein / TRANSFERASE-TRANSFERASE INHIBITOR complex

Function / homology

Function and homology information

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

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Tomchick, D.R. / Brautigam, C.A. / Deka, R.K. / Norgard, M.V.

Citation

Journal: Microbiologyopen / Year: 2016
Title: Molecular insights into the enzymatic diversity of flavin-trafficking protein (Ftp; formerly ApbE) in flavoprotein biogenesis in the bacterial periplasm.
Authors: Deka, R.K. / Brautigam, C.A. / Liu, W.Z. / Tomchick, D.R. / Norgard, M.V.

History

Deposition	Jan 2, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 16, 2016	Group: Database references
Revision 1.2	Nov 22, 2017	Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software Item: _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3	Sep 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4xgx.cif.gz	343.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4xgx.ent.gz	283.9 KB	Display	PDB format
PDBx/mmJSON format	4xgx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4xgx_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	4xgx_full_validation.pdf.gz	1.2 MB	Display
Data in XML	4xgx_validation.xml.gz	26.7 KB	Display
Data in CIF	4xgx_validation.cif.gz	38.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xg/4xgx ftp://data.pdbj.org/pub/pdb/validation_reports/xg/4xgx	HTTPS FTP

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Related structure data

Related structure data	4xgvSC 4xgwC 4xhfC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6zxu-1 6zy1-2 6zy1-1 2bf1-d 2x8z-d 6zxx-1 1m7w-1 4ras-1 2x93-d 6zxu-3 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

B: FAD:protein FMN transferase

hetero molecules

77 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	54.583, 56.981, 224.766
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	FAD:protein FMN transferase / Flavin transferase Mass: 37601.367 Da / Num. of mol.: 2 / Fragment: Soluble fragment (UNP residues 21-351) / Mutation: Y60N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: apbE, yojK, yojL, b2214, JW5368 / Plasmid: pET-21 NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AB85, FAD:protein FMN transferase

#1: Protein

FAD:protein FMN transferase / Flavin transferase

Mass: 37601.367 Da / Num. of mol.: 2 / Fragment: Soluble fragment (UNP residues 21-351) / Mutation: Y60N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K12 / Gene: apbE, yojK, yojL, b2214, JW5368 / Plasmid: pET-21 NESG / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AB85, FAD:protein FMN transferase

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Non-polymers , 5 types, 391 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#4: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: NO₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.32 Å³/Da / Density % sol: 47.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 5 mM magnesium chloride, 5 mM ADP, 0.2 M ammonium nitrate, 20% (w/v) PEG 3350, 35% (v/v) ethylene glycol;

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97918 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2013 / Details: monochromator

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.85→50 Å / Num. obs: 57017 / % possible obs: 93.6 % / Redundancy: 4.1 % / B_iso Wilson estimate: 19.09 Å² / R_merge(I) obs: 0.039 / R_pim(I) all: 0.02 / R_rim(I) all: 0.044 / Χ²: 0.932 / Net I/av σ(I): 29.6 / Net I/σ(I): 15.2 / Num. measured all: 231169

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.85-1.88	3.4	0.606	1856	0.719	0.334	0.698	0.919	60.7
1.88-1.92	3.6	0.515	2072	0.803	0.283	0.592	0.88	70.1
1.92-1.95	3.7	0.434	2317	0.852	0.239	0.499	0.922	76.5
1.95-1.99	3.9	0.367	2462	0.902	0.2	0.42	0.904	83.8
1.99-2.04	3.9	0.294	2768	0.937	0.161	0.337	0.901	91.2
2.04-2.08	4	0.241	2892	0.952	0.133	0.277	0.92	96.8
2.08-2.14	4.1	0.199	2955	0.97	0.109	0.228	0.941	98.6
2.14-2.19	4.1	0.165	3016	0.981	0.09	0.189	0.915	99.6
2.19-2.26	4.2	0.138	2994	0.983	0.075	0.158	0.898	99.9
2.26-2.33	4.2	0.104	3007	0.991	0.056	0.119	0.909	100
2.33-2.41	4.2	0.09	3017	0.992	0.048	0.102	0.921	100
2.41-2.51	4.2	0.072	3021	0.994	0.039	0.082	0.875	100
2.51-2.63	4.2	0.059	3052	0.996	0.031	0.067	0.847	100
2.63-2.76	4.2	0.05	3004	0.997	0.026	0.057	0.807	99.9
2.76-2.94	4.2	0.04	3065	0.998	0.021	0.045	0.852	99.9
2.94-3.16	4.2	0.039	3064	0.998	0.02	0.044	1.039	99.9
3.16-3.48	4.2	0.04	3033	0.997	0.02	0.045	1.382	99.6
3.48-3.99	4.1	0.037	3093	0.997	0.018	0.041	1.466	99.4
3.99-5.02	4	0.022	3102	0.999	0.012	0.025	0.805	98.7
5.02-50	3.9	0.017	3227	0.998	0.01	0.02	0.475	97

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Processing

Software

Name	Version	Classification
PHENIX		refinement
HKL-3000		data reduction
PDB_EXTRACT	3.15	data extraction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4XGV

4xgv

Resolution: 1.9→28.264 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2143	2495	5.01 %
R_work	0.1799	47349	-
obs	0.1816	49844	88.44 %

Solvent computation

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

Displacement parameters

B_iso max: 161.91 Å² / B_iso mean: 33.4323 Å² / B_iso min: 3.1 Å²

Refinement step

Cycle: final / Resolution: 1.9→28.264 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4470	0	158	372	5000
B_iso mean	-	-	42.07	35.05	-
Num. residues	-	-	-	-	583

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	4702
X-RAY DIFFRACTION	f_angle_d	0.985	6345
X-RAY DIFFRACTION	f_chiral_restr	0.035	731
X-RAY DIFFRACTION	f_plane_restr	0.004	806
X-RAY DIFFRACTION	f_dihedral_angle_d	14.864	1724

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9-1.9365	0.249	56	0.2263	1110	1166	38
1.9365-1.9761	0.2131	84	0.2229	1475	1559	50
1.9761-2.019	0.2708	107	0.2041	1867	1974	64
2.019-2.066	0.2173	107	0.21	2188	2295	75
2.066-2.1176	0.2737	127	0.1933	2420	2547	82
2.1176-2.1749	0.2535	136	0.1842	2613	2749	90
2.1749-2.2388	0.2438	161	0.1856	2805	2966	96
2.2388-2.3111	0.2283	151	0.1738	2940	3091	99
2.3111-2.3936	0.1955	134	0.1719	2978	3112	100
2.3936-2.4894	0.2019	153	0.1629	2950	3103	100
2.4894-2.6026	0.2232	161	0.169	2960	3121	100
2.6026-2.7397	0.2236	154	0.1826	2958	3112	100
2.7397-2.9112	0.21	132	0.1778	2973	3105	100
2.9112-3.1357	0.2523	142	0.189	3005	3147	100
3.1357-3.4508	0.2282	178	0.1822	2971	3149	100
3.4508-3.949	0.1858	174	0.1704	2999	3173	99
3.949-4.9709	0.1783	160	0.1581	3024	3184	99
4.9709-28.2675	0.2089	178	0.197	3113	3291	97

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	0.0072	-0.0072	0.0064	0.0058	-0.0041	0.0035	0.0029	-0.0004	-0.0128	0.0058	0.0163	-0.0303	0.0011	0.0231	0.0049	0.1313	-0.0827	-0.1301	0.3262	0.0113	0.1306	10.4586	21.0118	-12.5538
2	0.0001	-0.0018	-0.0002	0.0057	-0.0008	0.0007	0.0043	-0.0246	0.0121	0.0132	0.0048	-0.004	-0.0161	-0.0005	0.0023	0.2349	0.0031	0.0149	0.1683	-0.0528	0.0583	-11.2215	36.4104	-10.7797
3	0.0508	0.0081	0.0001	0.0289	-0.0238	0.0216	0.0204	-0.1665	-0.0335	0.0862	0.0543	0.0776	-0.0818	-0.1258	-0.007	0.0506	-0.0219	0.0976	0.0789	0.1777	-0.0696	-18.5145	26.795	-13.0423
4	0.0078	-0.0013	0.004	0.0033	0.0002	0.0021	0.0021	-0.0072	-0.0038	-0.0032	0.0158	-0.0102	-0.0022	0.0132	0.0279	0.0733	-0.0733	-0.068	0.2342	0.0561	0.0857	5.9541	19.5519	-20.3139
5	0.0251	-0.0275	0.0298	0.0538	-0.0253	0.0325	0.0164	-0.0452	-0.0358	0.0295	0.0714	0.0667	0.012	-0.0397	0.2017	0.063	-0.0455	-0.0032	0.1896	0.1791	0.0253	-6.4781	9.9859	-14.6374
6	0.0076	0.0066	0.0036	0.0142	0.0102	0.0082	-0.0308	-0.0164	-0.0312	0.029	-0.0097	0.0336	0.0399	0.0001	-0.0176	0.2469	-0.0935	0.0079	0.1325	0.1167	0.239	-13.6156	0.8301	-18.0737
7	0.0045	-0.0034	-0.0066	0.0076	-0.0003	0.0151	0.0051	0.0173	-0.0408	0.0071	0.0091	-0.0265	0.0177	0.0011	0.0144	0.1513	0.0378	0.006	0.0327	-0.0231	0.0865	-3.4159	5.9166	-46.0613
8	0.0045	-0.0024	0.0098	0.006	-0.0077	0.0259	-0.0233	0.0082	-0.056	-0.0039	-0.0113	0.0055	0.0281	-0.0119	-0.0207	0.1949	-0.0201	-0.0041	0.0431	-0.028	0.1526	-13.411	8.3389	-43.8036
9	0.0009	-0.0031	0.002	0.01	-0.0052	0.0041	0.0052	0.0056	-0.0048	-0.0157	0.003	0.0155	0.0005	-0.014	0.0061	0.1045	0.0646	-0.0505	0.1205	0.0465	0.0855	-21.1227	30.2843	-43.984
10	0.0031	-0.005	0.0023	0.0192	-0.0089	0.0043	-0.0135	0.0089	-0.0057	-0.0345	-0.0044	-0.002	-0.0338	0.0048	-0.011	0.0792	-0.0077	0.0486	0.0164	0.0602	0.1204	-6.5048	33.8465	-40.5426
11	0.0016	0.0023	-0.0052	0.0038	-0.0077	0.0157	0.0055	0.0074	-0.006	-0.0235	0.0115	0.0039	0.0046	-0.003	0.0163	0.2521	0.0123	0.0725	0.0792	0.0281	0.1336	-6.5664	44.1617	-55.9428
12	0.0115	-0.0167	-0.006	0.0331	0.0025	0.0071	0.0179	0.0057	-0.0043	-0.0305	0.0019	0.0042	-0.0259	-0.0267	0.0267	0.0896	0.0946	0.0671	0.0496	0.0699	0.1365	-15.811	34.1564	-36.6651
13	0.0079	0	0.0037	0.016	0.0024	0.0053	0.0221	-0.0108	-0.0641	0.0148	-0.0265	-0.0293	0.0206	0.0124	-0.0038	0.166	0.0319	0.0061	0.0229	0.0205	0.1233	-1.0728	9.291	-36.889
14	0.0227	0.0024	-0.0012	0.0008	0.0024	0.0178	0.0143	-0.0043	-0.0029	-0.028	0.0101	-0.0099	-0.009	0.0086	0.0434	0.1146	0.0323	0.0741	0.0719	0.0411	0.0776	5.4231	20.5815	-44.6481
15	0.0114	0.0188	-0.0159	0.0295	-0.0255	0.0221	0.0089	0.042	0.0347	-0.0445	-0.0058	-0.03	-0.0346	0.0182	-0.0155	0.0692	0.0069	0.1015	0.0728	0.0863	0.107	4.2885	31.2472	-43.3465
16	0.0093	0.0031	-0.0026	0.0047	-0.0017	0.001	-0.0023	0.0228	0.0234	-0.0163	-0.0121	-0.0206	-0.0098	0.0107	-0.0038	0.1063	-0.083	0.0335	0.2334	0.072	0.259	12.7641	32.2493	-39.2291
17	0.0267	-0.0022	-0.0092	0.0065	-0.005	0.0088	0.0114	0.0093	-0.013	-0.0048	0.001	-0.0069	-0.0017	0.0157	0.002	0.076	-0.0098	0.0363	0.2887	0.0629	0.2715	17.658	23.1926	-40.0127

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 57 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 81 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 82 through 167 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 168 through 192 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 193 through 289 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 290 through 329 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 13 through 35 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 36 through 57 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 58 through 81 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 82 through 113 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 114 through 136 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 137 through 167 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 168 through 209 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 210 through 255 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 256 through 289 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 290 through 311 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 312 through 329 )	B

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 391 molecules

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Viewer log

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This page

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Open data

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Download

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Validation report

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Related structure data

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Assembly

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 391 molecules

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Experimental details

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Experiment

-
Sample preparation

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Data collection

-
Processing

+
About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi