PDB-3ogh: Crystal structure of yciE protein from E. coli CFT073, a member o...

ID or keywords:

Entry

Database: PDB / ID: 3ogh

Title

Crystal structure of yciE protein from E. coli CFT073, a member of ferritine-like superfamily of diiron-containing four-helix-bundle proteins

Components

Protein yciE

Keywords

Structural Genomics / Unknown function / iron-binding / MCSG / four-helix-bundle / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Function and homology information

metal ion binding
Similarity search - Function

Biological species

Escherichia coli O6 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.65 Å

Authors

Nocek, B. / Bigelow, L. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of yciE protein from E. coli CFT073, a member of ferritine-like superfamily of diiron-containing four-helix-bundle proteins
Authors: Nocek, B. / Bigelow, L. / Bearden, J. / Joachimiak, A.

History

Deposition	Aug 16, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 15, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_leaving_atom_flag / _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_ref_seq_dif.details / _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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Download

PDBx/mmCIF format	3ogh.cif.gz	142.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3ogh.ent.gz	113 KB	Display	PDB format
PDBx/mmJSON format	3ogh.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/og/3ogh ftp://data.pdbj.org/pub/pdb/validation_reports/og/3ogh	HTTPS FTP

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Related structure data

Similar structure data	3hiu-2 1svs-d 6vme-2 3c5r-d 6vme-3 7bml-1 3qoq-d 5hxg-2 1svk-d 7nen-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: apc38261

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (1) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

B: Protein yciE

A: Protein yciE

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	30.148, 90.295, 58.132
Angle α, β, γ (deg.)	90.00, 103.51, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

AUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

#1: Protein	Protein yciE Mass: 19618.018 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O6 (bacteria) / Strain: CFT073 / Gene: yciE, c1723 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8FHW2, UniProt: A0A0H2V857*PLUS
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Nonpolymer details	THE AUTHORS BELIEVE THAT THE IRON ION LIKELY REPRESENTS IRON III, HOWEVER THERE IS NO EXPERIMENTAL ...THE AUTHORS BELIEVE THAT THE IRON ION LIKELY REPRESENTS IRON III, HOWEVER THERE IS NO EXPERIMENTAL DATA TO CONFIRM IT.

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.27 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% Peg 3350, 0.2 M Magnesium Chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2010 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.65→40 Å / Num. all: 36700 / Num. obs: 36634 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / R_merge(I) obs: 0.083 / Net I/σ(I): 29
Reflection shell	Resolution: 1.65→1.68 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.367 / Mean I/σ(I) obs: 4 / Num. unique all: 1843 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
SHELX		model building
ARP/wARP		model building
REFMAC	5.5.0109	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.65→40 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.952 / SU B: 3.437 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21291	1815	5 %	RANDOM
R_work	0.16648	-	-	-
all	0.18	36311	-	-
obs	0.16878	34496	99.46 %	-

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: 25.968 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.14 Å²	0 Å²	-0.91 Å²
2-	-	-1.96 Å²	0 Å²
3-	-	-	1.68 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2353	0	5	196	2554

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.021	2416
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1612
X-RAY DIFFRACTION	r_angle_refined_deg	1.794	1.943	3267
X-RAY DIFFRACTION	r_angle_other_deg	1.18	3	3957
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.869	5	302
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.453	25.126	119
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.441	15	452
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.732	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.115	0.2	372
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2673
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	453
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.88	1.5	1491
X-RAY DIFFRACTION	r_mcbond_other	5.601	1.5	595
X-RAY DIFFRACTION	r_mcangle_it	3.304	2	2406
X-RAY DIFFRACTION	r_scbond_it	4.221	3	925
X-RAY DIFFRACTION	r_scangle_it	6.65	4.5	856
X-RAY DIFFRACTION	r_rigid_bond_restr	2.408	3	2416
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.648→1.691 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.302	128	-
R_work	0.273	2477	-
obs	-	-	96.45 %

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	0.431	-0.1324	0.0004	1.2255	0.0109	0.5944	0.0086	-0.0942	0.023	0.1492	-0.0457	0.0624	-0.1047	-0.0544	0.0371	0.279	0.0058	-0.0024	0.2574	-0.0177	0.2553	13.7347	17.3745	28.5248
2	0.7992	-0.1228	-0.8897	12.1118	-0.3433	2.2906	-0.0238	0.005	-0.0371	0.4422	0.105	0.7187	0.066	0.014	-0.0813	0.2811	-0.0122	0.0248	0.2318	0.0124	0.282	14.0391	-2.9572	30.0535
3	2.3328	-5.1024	-2.7923	13.8532	5.0615	3.7555	-0.1138	0.02	-0.0819	0.0367	0.1324	0.5624	0.232	-0.0522	-0.0186	0.3677	-0.0602	-0.0699	0.216	0.0812	0.3399	16.8361	-15.5926	24.9859
4	1.1525	-1.0009	1.3925	2.7414	0.415	3.1614	0.0404	0.1018	-0.0479	0.2494	0.0056	0.0995	0.3133	0.3389	-0.046	0.2895	0.0179	-0.0064	0.2762	0.0268	0.2644	24.6878	-11.4599	25.5091
5	0.4033	-0.2275	-0.3977	1.9515	0.9101	0.6764	0.0073	-0.1112	0.0239	0.3477	-0.0104	-0.1022	0.0727	0.1162	0.0031	0.3444	-0.0281	-0.0493	0.2641	0.0007	0.2466	21.022	8.0162	35.4749
6	2.0575	-6.4844	0.1496	20.7369	1.2436	13.7262	0.4535	-0.0049	-0.2589	-1.1447	-0.2743	0.6615	1.7437	-0.5194	-0.1792	0.8151	-0.2363	-0.178	0.5786	0.3861	0.5357	8.4395	5.1283	31.2731
7	0.1305	-0.4028	-0.4667	3.0127	1.387	1.6835	-0.0482	-0.007	-0.0204	0.249	-0.052	0.0984	0.1467	-0.0137	0.1003	0.2517	-0.0088	0.0009	0.2476	0.0023	0.2614	16.4832	-6.31	17.2158
8	0.0854	0.0805	0.2726	1.901	0.5233	0.9173	-0.0471	0.0211	0.0064	0.1262	0.0463	-0.1145	-0.0831	0.0595	0.0008	0.2596	-0.0036	-0.0159	0.2483	-0.0137	0.2674	21.4022	14.185	23.6434
9	0.6048	1.3491	1.2549	5.0564	3.8826	3.178	-0.0591	0.1479	0.0973	0.0836	0.1724	-0.3943	0.0001	0.2247	-0.1133	0.2475	-0.0163	-0.0414	0.2692	-0.0077	0.3201	27.3902	7.5973	25.3514
10	1.1551	-1.0952	0.1924	2.4219	1.7225	2.722	-0.104	-0.0119	0.1049	0.1223	0.1494	-0.2449	0.0245	0.165	-0.0455	0.2356	0.0086	-0.013	0.2495	0.0008	0.3074	26.2614	-6.2951	17.0677
11	1.6084	2.1581	1.8144	6.3623	2.1823	2.4856	0.0411	0.0895	-0.135	0.2147	0.0439	-0.1984	0.1047	0.1566	-0.085	0.2444	0.0065	-0.0106	0.2437	0.0058	0.2617	23.0591	-14.952	11.6602
12	1.0208	0.4972	0.0568	4.3972	0.7244	2.7255	0.1279	-0.1142	-0.0889	0.3294	-0.0577	-0.0465	0.2514	0.0133	-0.0702	0.275	0.0005	-0.009	0.2391	0.0118	0.2624	17.7296	-24.314	12.24
13	0.7278	-0.739	-0.1554	2.3278	0.0832	0.4227	-0.0163	-0.0059	-0.1028	0.0618	0.0086	0.0842	0.0767	0.0004	0.0077	0.2147	-0.0017	-0.0023	0.2205	0.0021	0.2402	10.9765	-16.6553	3.7639
14	2.1194	-0.8419	-0.4476	5.6464	1.3352	0.3485	-0.0782	0.0386	0.0137	0.0327	0.0337	0.2811	0.002	-0.0055	0.0445	0.2323	0.0065	-0.0028	0.2461	0.0064	0.2755	5.1911	5.0344	3.4746
15	0.6997	-0.4067	0.0652	1.6932	1.1888	1.0481	-0.1308	-0.0125	-0.2091	0.0647	0.0143	0.3019	-0.0496	0.041	0.1164	0.2454	-0.001	0.0165	0.2392	-0.0029	0.3324	7.5947	19.3702	7.237
16	0.0205	0.1607	-0.0549	3.7603	0.0756	0.3348	-0.0233	0.0031	0.0089	-0.0138	0.0733	0.0322	-0.0406	0.0398	-0.05	0.2357	0.0013	-0.0029	0.2306	0.0003	0.2576	13.6854	15.0772	1.9452
17	0.2673	-0.0434	0.0443	3.2825	0.5531	0.1609	-0.0053	0.0518	-0.0255	-0.1777	0.0024	0.0326	-0.0125	0.0131	0.0029	0.2387	0.0014	-0.0039	0.2371	-0.0023	0.2546	11.5935	-3.8543	-5.5736
18	2.1593	-0.855	-0.7553	1.5429	0.1476	0.628	0.1205	0.0192	-0.0848	-0.0621	-0.0766	0.0251	0.0438	-0.1456	-0.0439	0.2205	0.0127	-0.0047	0.2219	-0.0065	0.2686	2.1351	-10.7693	-0.4724
19	3.5768	5.7395	2.1409	9.3948	3.5182	1.3302	-0.0296	-0.0025	0.1033	0.1892	0.0504	0.1359	0.0792	0.0152	-0.0208	0.261	0.0246	0.0165	0.3178	-0.0185	0.2708	2.2731	4.8704	11.9298
20	0.2657	-0.4808	-0.1704	2.4953	1.5591	1.0793	-0.0264	-0.0532	0.0136	0.0191	-0.0389	0.0921	-0.0446	-0.073	0.0653	0.2314	0	0.0108	0.2288	0.0029	0.2533	14.5156	4.2718	11.1955
21	0.3437	0.0567	-0.0561	1.2461	0.2226	0.5371	0.0131	0.0617	-0.058	-0.1053	0.0104	-0.0617	0.0599	0.0487	-0.0235	0.2141	0.0053	-0.0029	0.2361	-0.0058	0.2588	21.0093	-11.1871	-0.2991
22	0.5738	0.1494	-0.2214	5.1783	2.6763	3.0992	0.0041	0.0712	0.0179	-0.0773	0.0657	-0.1822	-0.0179	0.1581	-0.0698	0.211	-0.0011	-0.0012	0.2195	0.0052	0.2421	21.4663	4.3485	3.5089
23	0.2442	-0.2883	0.2107	1.3164	1.249	2.4833	0.0037	-0.0145	0.0343	-0.0846	0.0611	-0.1137	-0.1443	0.0543	-0.0648	0.2433	-0.0071	0.0119	0.234	-0.0048	0.2758	21.0279	14.7884	10.3879
24	0.9716	0.5278	-0.0205	1.8086	0.0435	2.5066	0.0295	0.025	0.1159	0.0708	0.0267	-0.0842	-0.2303	-0.0048	-0.0563	0.2695	0.0027	0.0026	0.2368	-0.0049	0.2605	15.0074	24.8387	17.2967

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 18
2	X-RAY DIFFRACTION	2	A	19 - 26
3	X-RAY DIFFRACTION	3	A	27 - 34
4	X-RAY DIFFRACTION	4	A	35 - 45
5	X-RAY DIFFRACTION	5	A	46 - 64
6	X-RAY DIFFRACTION	6	A	65 - 92
7	X-RAY DIFFRACTION	7	A	93 - 104
8	X-RAY DIFFRACTION	8	A	105 - 126
9	X-RAY DIFFRACTION	9	A	127 - 139
10	X-RAY DIFFRACTION	10	A	140 - 147
11	X-RAY DIFFRACTION	11	A	148 - 153
12	X-RAY DIFFRACTION	12	A	154 - 162
13	X-RAY DIFFRACTION	13	B	-2 - 18
14	X-RAY DIFFRACTION	14	B	19 - 27
15	X-RAY DIFFRACTION	15	B	28 - 35
16	X-RAY DIFFRACTION	16	B	36 - 45
17	X-RAY DIFFRACTION	17	B	46 - 63
18	X-RAY DIFFRACTION	18	B	64 - 73
19	X-RAY DIFFRACTION	19	B	74 - 92
20	X-RAY DIFFRACTION	20	B	93 - 111
21	X-RAY DIFFRACTION	21	B	112 - 134
22	X-RAY DIFFRACTION	22	B	135 - 142
23	X-RAY DIFFRACTION	23	B	143 - 150
24	X-RAY DIFFRACTION	24	B	151 - 160

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