PDB-3b8n: Structure of FepE- Bacterial Polysaccharide Co-polymerase

ID or keywords:

Entry

Database: PDB / ID: 3b8n

Title

Structure of FepE- Bacterial Polysaccharide Co-polymerase

Components

Ferric enterobactin (Enterochelin) transport

Keywords

BIOSYNTHETIC PROTEIN / WZZ / FepE / Bacterial Polysaccharide Co-polymerase / METAL TRANSPORT

Function / homology

Function and homology information

protein tyrosine kinase activity / identical protein binding / plasma membrane
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.1 Å

Authors

Tocilj, A. / Matte, A. / Cygler, M.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Bacterial polysaccharide co-polymerases share a common framework for control of polymer length
Authors: Tocilj, A. / Munger, C. / Proteau, A. / Morona, R. / Purins, L. / Ajamian, E. / Wagner, J. / Papadopoulos, M. / Van Den Bosch, L. / Rubinstein, J.L. / Fethiere, J. / Matte, A. / Cygler, M.

History

Deposition	Nov 1, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 22, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3b8n.cif.gz	419.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3b8n.ent.gz	346.9 KB	Display	PDB format
PDBx/mmJSON format	3b8n.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/b8/3b8n ftp://data.pdbj.org/pub/pdb/validation_reports/b8/3b8n	HTTPS FTP

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Related structure data

Related structure data	3b8mC 3b8oC 3b8pC C: citing same article (ref.)
Similar structure data	4e2l-d 3b8m-1 5019 6lcl-1 6623 1930 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

Deposited unit

A: Ferric enterobactin (Enterochelin) transport

B: Ferric enterobactin (Enterochelin) transport

C: Ferric enterobactin (Enterochelin) transport

D: Ferric enterobactin (Enterochelin) transport

E: Ferric enterobactin (Enterochelin) transport

F: Ferric enterobactin (Enterochelin) transport

G: Ferric enterobactin (Enterochelin) transport

H: Ferric enterobactin (Enterochelin) transport

I: Ferric enterobactin (Enterochelin) transport

286 kDa, 9 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)	160.670, 160.670, 276.938
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 3 / Auth seq-ID: 65 - 330 / Label seq-ID: 13 - 278

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

#1: Protein	Ferric enterobactin (Enterochelin) transport Mass: 31735.908 Da / Num. of mol.: 9 / Fragment: residues 65-331 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: fepE / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8XBV8

#1: Protein

Ferric enterobactin (Enterochelin) transport

Mass: 31735.908 Da / Num. of mol.: 9 / Fragment: residues 65-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: O157:H7 / Gene: fepE / Plasmid: pET15b / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8XBV8

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.612717 Å³/Da / Density % sol: 70.5 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: Sodium Citrate Na3C6H5O7, pH 7.5, vapor diffusion, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 0.98 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Redundancy: 3.8 % / Av σ(I) over netI: 6.6 / Number: 413237 / R_merge(I) obs: 0.167 / Χ²: 1.67 / D res high: 3.37 Å / D res low: 50 Å / Num. obs: 109859 / % possible obs: 99.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
7.25	50	98.6	1	0.036	1.645	3.8
5.76	7.25	99.9	1	0.109	1.607	3.9
5.03	5.76	99.9	1	0.15	1.734	3.9
4.57	5.03	99.9	1	0.163	1.78	3.9
4.25	4.57	99.8	1	0.215	1.734	3.9
4	4.25	99.9	1	0.301	1.685	3.9
3.8	4	99.9	1	0.418	1.677	3.9
3.63	3.8	99.9	1	0.558	1.635	3.8
3.49	3.63	99.9	1	0.763	1.611	3.6
3.37	3.49	98.8	1	0.973	1.539	3.1

Reflection

Resolution: 3→20 Å / Num. obs: 83083 / % possible obs: 99.8 % / Redundancy: 8.3 % / R_merge(I) obs: 0.078 / Χ²: 1.055 / Net I/σ(I): 9.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
3-3.11	7.7	0.365	8240	0.488	1	100
3.11-3.23	8.4	0.265	8241	0.53	1	100
3.23-3.38	8.4	0.199	8226	0.573	1	100
3.38-3.55	8.4	0.151	8258	0.672	1	100
3.55-3.78	8.3	0.123	8259	0.982	1	100
3.78-4.06	8.3	0.093	8276	1.083	1	99.9
4.06-4.47	8.3	0.074	8315	1.287	1	99.8
4.47-5.11	8.4	0.068	8325	1.647	1	99.8
5.11-6.4	8.6	0.068	8390	1.601	1	99.5
6.4-20	8.7	0.037	8553	1.571	1	98.6

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Phasing

Phasing

Method:

SAD

Phasing MAD set

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Lowest resolution (Å)	Reflection acentric	Reflection centric
ISO_1	0	0	3.8	48.74	36036	3728
ANO_1	0.868	0	3.8	48.74	35994	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	Reflection acentric	Reflection centric
ISO_1	16.1-48.74	0	387	165
ISO_1	11.71-16.1	0	690	174
ISO_1	9.65-11.71	0	912	155
ISO_1	8.4-9.65	0	1101	165
ISO_1	7.53-8.4	0	1266	170
ISO_1	6.89-7.53	0	1408	180
ISO_1	6.39-6.89	0	1534	192
ISO_1	5.98-6.39	0	1644	187
ISO_1	5.65-5.98	0	1775	196
ISO_1	5.36-5.65	0	1881	197
ISO_1	5.11-5.36	0	1947	197
ISO_1	4.9-5.11	0	2038	189
ISO_1	4.71-4.9	0	2171	199
ISO_1	4.54-4.71	0	2215	186
ISO_1	4.39-4.54	0	2320	196
ISO_1	4.25-4.39	0	2383	196
ISO_1	4.12-4.25	0	2474	198
ISO_1	4.01-4.12	0	2567	182
ISO_1	3.9-4.01	0	2618	197
ISO_1	3.8-3.9	0	2705	207
ANO_1	16.1-48.74	0.224	379	0
ANO_1	11.71-16.1	0.283	689	0
ANO_1	9.65-11.71	0.401	910	0
ANO_1	8.4-9.65	0.432	1101	0
ANO_1	7.53-8.4	0.527	1265	0
ANO_1	6.89-7.53	0.62	1407	0
ANO_1	6.39-6.89	0.719	1533	0
ANO_1	5.98-6.39	0.755	1642	0
ANO_1	5.65-5.98	0.814	1772	0
ANO_1	5.36-5.65	0.852	1880	0
ANO_1	5.11-5.36	0.861	1945	0
ANO_1	4.9-5.11	0.909	2035	0
ANO_1	4.71-4.9	0.914	2169	0
ANO_1	4.54-4.71	0.927	2211	0
ANO_1	4.39-4.54	0.948	2319	0
ANO_1	4.25-4.39	0.968	2381	0
ANO_1	4.12-4.25	0.973	2472	0
ANO_1	4.01-4.12	0.98	2565	0
ANO_1	3.9-4.01	0.985	2616	0
ANO_1	3.8-3.9	0.989	2703	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	50.764	117.081	2.833	SE	103.67	0.22
2	35.065	83.742	43.666	SE	117.73	0.25
3	62.301	71.811	40.432	SE	124.55	0.26
4	47.034	106.427	29.933	SE	81.52	0.2
5	100.429	29.233	21.319	SE	131.31	0.19
6	101.167	78.7	38.739	SE	170.28	0.21
7	36.033	31.04	14.418	SE	92.38	0.22
8	20.329	59.387	37.742	SE	92.18	0.24
9	10.34	44.659	14.959	SE	98.22	0.22
10	73.613	94.01	25.012	SE	85.6	0.2
11	41.397	34.548	43.121	SE	127.33	0.15
12	83.674	113.541	5.123	SE	173.47	0.18
13	47.384	46.951	35.797	SE	140.99	0.25
14	120.958	45.942	37.012	SE	82.77	0.18
15	-8.728	122.438	28.182	SE	200.43	0.21
16	6.201	35.689	26.803	SE	172.03	0.2
17	28.421	17.988	10.783	SE	92.13	0.16
18	110.529	46.006	20.462	SE	122.86	0.17
19	77.355	97.486	39.472	SE	217.46	0.22
20	-17.303	105.779	34.451	SE	206.55	0.24
21	92.231	16.858	9.664	SE	165.21	0.21
22	55.109	120.3	32.324	SE	268.55	0.19
23	117.377	59.507	8.285	SE	300	0.14
24	-15.341	70.59	32.943	SE	223.25	0.12
25	-32.561	84.31	9.265	SE	261.96	0.19
26	-5.366	131.509	11.53	SE	229.36	0.19
27	116.358	58.955	7.46	SE	1	0.05
28	-27.127	91.123	26.933	SE	153.13	0.17
29	-19.694	72.147	37.682	SE	66.85	0.06
30	135.919	38.95	9.281	SE	1	0.02

Phasing dm

FOM : 0.71 / FOM acentric: 0.71 / FOM centric: 0.67 / Reflection: 48129 / Reflection acentric: 43823 / Reflection centric: 4306

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
9.7-29.968	0.95	0.97	0.9	2455	1934	521
6.1-9.7	0.88	0.88	0.84	7533	6615	918
4.9-6.1	0.8	0.81	0.68	9372	8505	867
4.3-4.9	0.79	0.79	0.68	9377	8646	731
3.6-4.3	0.62	0.62	0.54	14056	13133	923
3.4-3.6	0.29	0.3	0.25	5336	4990	346

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
SHARP		phasing
RESOLVE	2.1	phasing
REFMAC	refmac_5.2.0019	refinement
PDB_EXTRACT	2	data extraction
DENZO		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 3.1→20 Å / Cor.coef. F_o:F_c: 0.906 / Cor.coef. F_o:F_c free: 0.868 / WR_factor R_free: 0.262 / WR_factor R_work: 0.233 / SU B: 20.081 / SU ML: 0.356 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.825 / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.282	3751	5 %	RANDOM
R_work	0.254	-	-	-
all	0.256	-	-	-
obs	-	75106	99.69 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 60.348 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.62 Å²	0.31 Å²	0 Å²
2-	-	0.62 Å²	0 Å²
3-	-	-	-0.93 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17478	0	0	0	17478

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	17766
X-RAY DIFFRACTION	r_angle_refined_deg	1.396	1.979	24039
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.39	5	2133
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.528	25.435	828
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.396	15	3330
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.071	15	90
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	2799
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	13077
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	7987
X-RAY DIFFRACTION	r_nbtor_refined	0.315	0.2	12221
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	253
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.313	0.2	39
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.221	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.41	1.5	11114
X-RAY DIFFRACTION	r_mcangle_it	0.779	2	17658
X-RAY DIFFRACTION	r_scbond_it	1.486	3	7456
X-RAY DIFFRACTION	r_scangle_it	2.512	4.5	6381

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	A	964	TIGHT POSITIONAL	0.04	0.05
2	B	964	TIGHT POSITIONAL	0.05	0.05
3	C	964	TIGHT POSITIONAL	0.04	0.05
4	D	964	TIGHT POSITIONAL	0.04	0.05
5	E	964	TIGHT POSITIONAL	0.04	0.05
6	F	964	TIGHT POSITIONAL	0.06	0.05
7	G	964	TIGHT POSITIONAL	0.05	0.05
8	H	964	TIGHT POSITIONAL	0.04	0.05
9	I	964	TIGHT POSITIONAL	0.05	0.05
1	A	979	LOOSE POSITIONAL	0.45	5
2	B	979	LOOSE POSITIONAL	0.47	5
3	C	979	LOOSE POSITIONAL	0.5	5
4	D	979	LOOSE POSITIONAL	0.43	5
5	E	979	LOOSE POSITIONAL	0.43	5
6	F	979	LOOSE POSITIONAL	0.62	5
7	G	979	LOOSE POSITIONAL	0.45	5
8	H	979	LOOSE POSITIONAL	0.45	5
9	I	979	LOOSE POSITIONAL	0.53	5
1	A	964	TIGHT THERMAL	0.06	0.5
2	B	964	TIGHT THERMAL	0.07	0.5
3	C	964	TIGHT THERMAL	0.07	0.5
4	D	964	TIGHT THERMAL	0.08	0.5
5	E	964	TIGHT THERMAL	0.06	0.5
6	F	964	TIGHT THERMAL	0.07	0.5
7	G	964	TIGHT THERMAL	0.07	0.5
8	H	964	TIGHT THERMAL	0.07	0.5
9	I	964	TIGHT THERMAL	0.06	0.5
1	A	979	LOOSE THERMAL	1.5	10
2	B	979	LOOSE THERMAL	1.98	10
3	C	979	LOOSE THERMAL	1.73	10
4	D	979	LOOSE THERMAL	1.69	10
5	E	979	LOOSE THERMAL	1.23	10
6	F	979	LOOSE THERMAL	1.68	10
7	G	979	LOOSE THERMAL	1.52	10
8	H	979	LOOSE THERMAL	1.51	10
9	I	979	LOOSE THERMAL	1.4	10

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	Num. reflection all	% reflection obs (%)
3.1-3.179	0.385	286	0.317	5081	5367	100
3.179-3.263	0.362	268	0.308	5033	5303	99.962
3.263-3.355	0.348	232	0.313	4883	5118	99.941
3.355-3.456	0.326	260	0.288	4718	4980	99.96
3.456-3.565	0.346	235	0.281	4645	4885	99.898
3.565-3.686	0.282	234	0.264	4417	4656	99.893
3.686-3.82	0.324	216	0.267	4343	4567	99.825
3.82-3.97	0.292	213	0.259	4152	4378	99.703
3.97-4.14	0.278	211	0.246	3979	4201	99.738
4.14-4.332	0.273	192	0.251	3848	4050	99.753
4.332-4.555	0.279	195	0.235	3639	3849	99.61
4.555-4.816	0.26	191	0.231	3461	3661	99.754
4.816-5.127	0.251	176	0.229	3283	3469	99.712
5.127-5.508	0.32	159	0.267	3104	3269	99.816
5.508-5.988	0.32	148	0.303	2859	3019	99.603
5.988-6.621	0.351	129	0.263	2634	2783	99.281
6.621-7.509	0.266	133	0.243	2329	2481	99.234
7.509-8.889	0.257	106	0.196	2064	2194	98.906
8.889-11.488	0.189	96	0.174	1675	1803	98.225
11.488-20	0.225	71	0.238	1208	1304	98.083

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