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

ID or keywords:

Entry

Database: PDB / ID: 4xgw

Title

Crystal structure of Escherichia coli Flavin trafficking protein, an FMN transferase, E169K mutant

Components

FAD:protein FMN transferase

Keywords

TRANSFERASE / FLAVIN TRANSFERASE / BIMETAL CENTER / LIPOPROTEIN

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 /

FOURIER SYNTHESIS / Resolution: 1.747 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	Dec 23, 2015	Group: Derived calculations
Revision 1.2	Mar 16, 2016	Group: Database references
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 / pdbx_struct_oper_list / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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 / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4xgw.cif.gz	690.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4xgw.ent.gz	584.5 KB	Display	PDB format
PDBx/mmJSON format	4xgw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xg/4xgw ftp://data.pdbj.org/pub/pdb/validation_reports/xg/4xgw	HTTPS FTP

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Related structure data

Related structure data	4xgvSC 4xgxC 4xhfC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5i56-d 6uzg-d 6fm2-d 6vxe-2 5dlg-d 4ed6-d 5f9n-d 3du4-d 6o5h-3 5h8q-d 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

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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

C: FAD:protein FMN transferase

D: FAD:protein FMN transferase

hetero molecules

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

1

A: FAD:protein FMN transferase

C: FAD:protein FMN transferase

hetero molecules

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

2

B: FAD:protein FMN transferase

D: FAD:protein FMN transferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	57.216, 70.650, 86.276
Angle α, β, γ (deg.)	75.720, 71.910, 69.720
Int Tables number	1
Space group name H-M	P1

#1: Protein	FAD:protein FMN transferase / Flavin transferase Mass: 37650.504 Da / Num. of mol.: 4 / Fragment: Soluble fragment, UNP residues 21-351 / Mutation: E169K 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
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 679 / 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: 2.04 Å³/Da / Density % sol: 39.64 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M NaCl, 25% (w/v) PEG 3350, 0.1 M HEPES, 20% (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: Nov 2, 2012 / 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: 1.747→50 Å / Num. all: 116958 / Num. obs: 116958 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / R_merge(I) obs: 0.087 / Χ²: 1.493 / Net I/av σ(I): 20.748 / Net I/σ(I): 10.3 / Num. measured all: 429538

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
1.75-1.78	3.6	0.855	1.8	5748	1.4	96
1.78-1.81	3.6	0.813		5783	1.539	96.1
1.81-1.85	3.7	0.696		5833	1.532	96.2
1.85-1.89	3.7	0.611		5722	1.571	96.1
1.89-1.93	3.7	0.491		5818	1.662	96.4
1.93-1.97	3.7	0.4		5831	1.63	96.6
1.97-2.02	3.7	0.313		5829	1.21	96.7
2.02-2.07	3.7	0.273		5777	1.282	96.8
2.07-2.14	3.7	0.227		5819	1.272	96.9
2.14-2.2	3.7	0.194		5893	1.193	97.4
2.2-2.28	3.7	0.184		5834	1.511	97.1
2.28-2.38	3.7	0.138		5873	1.288	97.4
2.38-2.48	3.7	0.124		5868	1.419	97.8
2.48-2.61	3.7	0.105		5889	1.351	97.8
2.61-2.78	3.7	0.094		5864	1.511	98.1
2.78-2.99	3.7	0.074		5906	1.606	98.3
2.99-3.29	3.6	0.057		5912	1.578	98.6
3.29-3.77	3.5	0.045		5967	1.846	98.7
3.77-4.75	3.6	0.035		5945	1.782	98.8
4.75-50	3.7	0.033		5847	1.709	97.4

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Processing

Software

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

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 4XGV

4xgv

Resolution: 1.747→33.922 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1985	5873	5.04 %	random selection
R_work	0.1718	110687	-	-
obs	0.1732	116560	96.55 %	-

Solvent computation

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

Displacement parameters

B_iso max: 177.48 Å² / B_iso mean: 34.1684 Å² / B_iso min: 11.79 Å²

Refinement step

Cycle: final / Resolution: 1.747→33.922 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9432	0	47	679	10158
B_iso mean	-	-	50.34	31.13	-
Num. residues	-	-	-	-	1222

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	9671
X-RAY DIFFRACTION	f_angle_d	0.874	13101
X-RAY DIFFRACTION	f_chiral_restr	0.033	1487
X-RAY DIFFRACTION	f_plane_restr	0.004	1676
X-RAY DIFFRACTION	f_dihedral_angle_d	12.653	3579

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7466-1.7664	0.2998	188	0.244	3192	3380	84
1.7664-1.7872	0.2712	176	0.2519	3667	3843	95
1.7872-1.809	0.285	168	0.2512	3637	3805	95
1.809-1.8319	0.3016	169	0.2579	3672	3841	95
1.8319-1.856	0.2732	199	0.2385	3645	3844	95
1.856-1.8814	0.2921	162	0.2356	3643	3805	96
1.8814-1.9083	0.2465	181	0.2184	3689	3870	95
1.9083-1.9368	0.227	215	0.2047	3593	3808	96
1.9368-1.967	0.2297	209	0.1948	3710	3919	96
1.967-1.9993	0.2115	192	0.1819	3664	3856	96
1.9993-2.0337	0.2217	181	0.182	3724	3905	97
2.0337-2.0707	0.2187	192	0.1831	3695	3887	97
2.0707-2.1105	0.22	218	0.176	3692	3910	97
2.1105-2.1536	0.1915	196	0.166	3659	3855	97
2.1536-2.2004	0.1802	217	0.1679	3720	3937	97
2.2004-2.2516	0.2117	179	0.1722	3667	3846	97
2.2516-2.3079	0.1871	188	0.1643	3759	3947	97
2.3079-2.3703	0.2	207	0.1637	3716	3923	97
2.3703-2.44	0.2013	193	0.1619	3719	3912	98
2.44-2.5187	0.2095	193	0.1586	3729	3922	98
2.5187-2.6087	0.1782	205	0.1676	3778	3983	98
2.6087-2.7131	0.2288	194	0.1764	3739	3933	98
2.7131-2.8366	0.2089	210	0.1772	3708	3918	98
2.8366-2.986	0.1901	212	0.1808	3728	3940	98
2.986-3.173	0.2017	192	0.1803	3799	3991	99
3.173-3.4178	0.206	214	0.1742	3721	3935	99
3.4178-3.7613	0.1884	203	0.1614	3800	4003	99
3.7613-4.3046	0.1672	210	0.148	3741	3951	99
4.3046-5.4198	0.1606	185	0.1337	3813	3998	99
5.4198-33.9279	0.1648	225	0.1617	3668	3893	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	2.2178	-1.072	0.1617	1.1345	-0.2749	0.8464	-0.0813	-0.2539	-0.0901	0.1547	0.0317	0.1033	-0.0065	-0.0554	0.0473	0.1895	-0.0102	0.0271	0.236	-0.0047	0.163	43.7043	1.6607	3.2641
2	0.4099	0.7534	-0.1367	2.0926	0.2612	0.8353	0.064	-0.1408	0.0108	0.156	-0.0766	-0.1329	0.0197	0.0945	0.0222	0.1332	0.0048	-0.0265	0.2298	0.0194	0.2019	64.1803	6.8971	-0.6433
3	1.4156	0.3577	0.1077	0.735	-0.0143	0.8274	-0.0039	-0.0794	0.2098	-0.0088	-0.0557	0.0979	-0.1197	-0.0135	0.0692	0.1595	0.0056	-0.0055	0.1643	-0.0263	0.1694	47.9801	16.0657	-11.184
4	2.2261	1.527	0.3656	5.0685	-0.0329	2.1029	0.0208	-0.1144	-0.1209	0.3577	0.0869	0.1323	-0.1214	-0.1962	-0.0437	0.3063	-0.0161	0.0329	0.2128	0.0104	0.1763	44.8004	28.8447	-36.3422
5	1.317	0.9361	-0.8643	1.0821	-0.599	1.7138	0.1471	-0.2142	0.0164	0.2528	-0.128	-0.0869	-0.1275	0.3085	0.0174	0.2731	-0.0245	-0.0437	0.2389	-0.0055	0.1848	63.2939	35.2921	-42.5976
6	1.0927	0.0452	-0.2017	0.9177	0.2516	0.8471	0.0713	-0.0862	0.2857	0.1008	-0.0061	-0.1084	-0.2391	0.125	-0.0708	0.2363	-0.0432	-0.0076	0.1694	-0.0309	0.19	59.745	46.8694	-51.5949
7	2.0919	-0.4184	0.3612	1.9211	0.1594	1.9576	0.0366	-0.1588	-0.0267	0.3193	-0.0236	0.2545	-0.0764	-0.319	-0.0418	0.2012	0.0086	0.0564	0.171	-0.0084	0.1857	37.831	31.2011	-46.5107
8	0.9913	0.6111	0.0924	2.0079	0.4644	0.9641	0.0857	0.0015	0.2768	0.2428	-0.0629	0.2841	-0.2873	-0.121	-0.0082	0.3027	0.0335	0.0273	0.157	0.0016	0.2663	41.3261	51.2297	-52.3597
9	2.357	-2.1221	0.1487	6.503	-0.6344	2.0621	0.0221	0.2451	-0.1048	-0.3572	-0.0621	0.3297	0.2716	0.005	0.0452	0.3131	0.0286	0.019	0.2354	0.0162	0.173	44.0682	-0.1288	-36.6717
10	2.5319	-1.8033	1.7435	1.7045	-1.2536	1.6956	0.1982	0.266	0.0055	-0.5048	-0.2986	-0.192	0.4318	0.387	0.0548	0.3409	0.098	0.1085	0.2818	0.0443	0.1806	62.0046	-7.1121	-29.6353
11	1.2894	-0.1235	0.1031	0.7692	0.0623	0.899	0.0141	0.1158	-0.2298	-0.2166	-0.0535	-0.1232	0.4241	0.1489	0.0143	0.3589	0.0673	0.0425	0.187	0.0077	0.1925	59.7679	-21.2017	-18.0688
12	0.7377	-0.1806	-0.3771	2.0565	-0.2439	1.4494	0.0071	0.1206	-0.0384	-0.2407	-0.0731	0.2225	0.1999	-0.1089	0.0366	0.2339	0.0053	-0.0185	0.1799	-0.0179	0.1496	40.4361	-2.6384	-26.2372
13	1.323	-0.7922	0.908	0.543	-0.5123	0.7756	0.3324	0.0214	-0.2629	-0.3293	-0.0007	0.064	0.7748	-0.1709	-0.0684	0.6982	-0.0272	-0.031	0.2928	-0.0326	0.3129	41.3532	-30.1779	-28.2015
14	0.6417	-0.0048	-0.0301	1.2692	0.1991	0.4996	0.1415	0.0131	-0.1317	-0.1238	-0.1107	-0.0536	0.4238	0.0042	-0.0298	0.3848	0.0008	-0.0195	0.1664	-0.0096	0.1837	44.4131	-21.1409	-19.3753
15	1.1443	0.3777	0.1432	2.373	0.7051	1.1566	0.1878	-0.1538	-0.0513	0.0437	-0.1862	0.3387	0.3909	-0.2038	-0.0272	0.3597	-0.1216	0.0016	0.24	-0.0119	0.2237	33.564	-19.1742	-16.1325
16	0.2976	0.0502	-0.011	0.8206	-0.114	1.0199	0.0091	0.1002	0.0503	-0.0743	0.0039	0.095	0.0229	-0.084	0.0046	0.1253	-0.0092	-0.0084	0.1852	0.0072	0.1532	48.4223	27.9895	-73.9767
17	1.6238	-0.447	-0.88	3.3651	1.2306	2.7453	0.0779	-0.0429	-0.0987	-0.3756	0.0178	-0.0685	0.0203	0.0996	-0.1053	0.1998	0.0417	-0.0061	0.218	0.0048	0.1985	68.1867	12.4913	-77.2792
18	1.1339	-0.0446	-0.4131	0.6692	0.0883	0.803	-0.0448	0.1014	-0.0345	-0.0077	0.0174	0.0744	-0.0021	-0.035	0.0214	0.0931	-0.0077	-0.0091	0.1529	0.0037	0.1256	50.2219	27.5992	-66.9192
19	1.9321	-0.8193	-0.6603	1.1981	0.581	1.199	-0.0042	0.0919	-0.2325	0.0229	-0.0435	0.0396	0.107	0.0621	0.0465	0.1799	0.0076	-0.0014	0.1773	-0.0094	0.1709	55.3223	10.6005	-62.8783
20	2.9396	0.4881	0.1897	2.8687	0.5112	3.284	-0.0439	0.0012	-0.4362	0.2163	0.1264	0.046	0.5155	-0.0059	0.0596	0.2638	-0.0122	0.0099	0.1386	0.0144	0.2178	49.2942	5.5868	-55.6659

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 81 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 82 through 167 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 168 through 328 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 13 through 35 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 36 through 81 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 82 through 183 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 184 through 230 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 231 through 328 )	B
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 13 through 35 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 36 through 81 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 82 through 167 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 168 through 236 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 237 through 256 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 257 through 289 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 290 through 329 )	C
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 13 through 98 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 99 through 136 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 137 through 209 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 210 through 301 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 302 through 329 )	D

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

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Yorodumi