PDB-7oah: conserved hypothetical protein residues 311-335 from Candidatus M...

ID or keywords:

Entry

Database: PDB / ID: 7oah

Title

conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors, mutant beta2/A

Components

General control transcription factor GCN4,conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors, mutant beta2/A,General control transcription factor GCN4

Keywords

PROTEIN FIBRIL / Coiled Coil / beta layer / hexad repeat

Function / homology

Function and homology information

protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Candidatus Magnetomorum sp. HK-1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.694 Å

Authors

Adlakha, J. / Albrecht, R. / Hartmann, M.D.

Citation

Journal: To Be Published
Title: conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors, mutant beta2/A
Authors: Adlakha, J.

History

Deposition	Apr 19, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 4, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7oah.cif.gz	210.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7oah.ent.gz	168.3 KB	Display	PDB format
PDBx/mmJSON format	7oah.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7oah_validation.pdf.gz	457.2 KB	Display	wwPDB validaton report
Full document	7oah_full_validation.pdf.gz	461.7 KB	Display
Data in XML	7oah_validation.xml.gz	12.7 KB	Display
Data in CIF	7oah_validation.cif.gz	17.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oa/7oah ftp://data.pdbj.org/pub/pdb/validation_reports/oa/7oah	HTTPS FTP

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Related structure data

Related structure data	7oaaS S: Starting model for refinement
Similar structure data	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	#70 - Oct 2005 Designer Proteins similarity (9) #122 - Feb 2010 Enhanceosome similarity (4)

Deposited unit

A: General control transcription factor GCN4,conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors, mutant beta2/A,General control transcription factor GCN4

B: General control transcription factor GCN4,conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors, mutant beta2/A,General control transcription factor GCN4

C: General control transcription factor GCN4,conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors, mutant beta2/A,General control transcription factor GCN4

hetero molecules

30 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	26.126, 38.769, 132.277
Angle α, β, γ (deg.)	90.000, 94.846, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	B
2	3	C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	LYS	LYS	A	A	281 - 361	4 - 84
2	1	SER	SER	LYS	LYS	B	B	281 - 361	4 - 84
1	2	GLY	GLY	ILE	ILE	A	A	282 - 360	5 - 83
2	2	GLY	GLY	ILE	ILE	C	C	282 - 360	5 - 83
1	3	GLY	GLY	ILE	ILE	B	B	282 - 360	5 - 83
2	3	GLY	GLY	ILE	ILE	C	C	282 - 360	5 - 83

NCS ensembles :

ID
1
2
3

#1: Protein	General control transcription factor GCN4,conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors, mutant beta2/A,General control transcription factor GCN4 / Amino acid biosynthesis regulatory protein / General control protein GCN4 Mass: 9951.712 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Candidatus Magnetomorum sp. HK-1 (bacteria) Strain: ATCC 204508 / S288c / Gene: GCN4, AAS101, AAS3, ARG9, YEL009C, MHK_004959 / Production host: Escherichia coli (E. coli) / References: UniProt: P03069, UniProt: A0A0N0D484
#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 44.99 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.1 M tri-sodium citrate pH 5.5, 20% (w/v) PEG 3000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.69→37.19 Å / Num. obs: 29121 / % possible obs: 97.9 % / Redundancy: 6.66 % / CC_1/2: 1 / R_merge(I) obs: 0.082 / Net I/σ(I): 13.73
Reflection shell	Resolution: 1.69→1.8 Å / Redundancy: 6.76 % / R_merge(I) obs: 0.912 / Mean I/σ(I) obs: 1.78 / Num. unique obs: 4428 / CC_1/2: 0.86 / % possible all: 92.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049 2013/06/30	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7OAA

7oaa

Resolution: 1.694→37.19 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.918 / SU B: 5.979 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.132
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2678	1456	-
R_work	0.2204	27662	-
all	0.223	-	-
obs	-	29118	97.902 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 34.516 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.799 Å²	-0 Å²	-1.263 Å²
2-	-	0.164 Å²	0 Å²
3-	-	-	0.837 Å²

Refinement step

Cycle: LAST / Resolution: 1.694→37.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2010	0	13	166	2189

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	2098
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	2218
X-RAY DIFFRACTION	r_angle_refined_deg	1.008	1.98	2808
X-RAY DIFFRACTION	r_angle_other_deg	1.103	3	5155
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.232	5	261
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.442	27.033	91
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.469	15	497
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.94	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	329
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	2255
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	399
X-RAY DIFFRACTION	r_nbd_refined	0.237	0.2	611
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.14	0.2	1955
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	975
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1118
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.131	0.2	27
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.203	0.2	73
X-RAY DIFFRACTION	r_nbd_other	0.194	0.2	142
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.291	0.2	10
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.042	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	2.448	6.682	999
X-RAY DIFFRACTION	r_mcbond_other	2.438	6.66	998
X-RAY DIFFRACTION	r_mcangle_it	3.427	11.129	1251
X-RAY DIFFRACTION	r_mcangle_other	3.429	11.153	1252
X-RAY DIFFRACTION	r_scbond_it	4.324	8.783	1099
X-RAY DIFFRACTION	r_scbond_other	4.323	8.781	1099
X-RAY DIFFRACTION	r_scangle_it	6.553	13.772	1549
X-RAY DIFFRACTION	r_scangle_other	6.552	13.767	1549
X-RAY DIFFRACTION	r_lrange_it	8.43	32.041	2523
X-RAY DIFFRACTION	r_lrange_other	8.406	31.147	2465
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.182	0.05	4041
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.167	0.05	3953
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.161	0.05	4021

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	4041	0.18
1	2	B	4041	0.18
2	1	A	3953	0.17
2	2	C	3953	0.17
3	1	B	4021	0.16
3	2	C	4021	0.16

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 (%)	WR_factor R_work
1.694-1.738	0.333	96	0.404	1826	2217	86.6937	0.377
1.738-1.785	0.337	102	0.342	1943	2097	97.5203	0.31
1.785-1.837	0.345	100	0.314	1903	2054	97.517	0.277
1.837-1.893	0.349	100	0.287	1903	2023	99.0114	0.243
1.893-1.955	0.291	94	0.261	1789	1933	97.4133	0.214
1.955-2.024	0.271	95	0.224	1803	1915	99.1123	0.191
2.024-2.1	0.245	88	0.219	1664	1778	98.5377	0.192
2.1-2.185	0.223	87	0.215	1658	1776	98.2545	0.194
2.185-2.282	0.242	82	0.186	1548	1652	98.6683	0.171
2.282-2.393	0.238	81	0.199	1544	1628	99.8157	0.181
2.393-2.522	0.255	75	0.195	1421	1515	98.7459	0.178
2.522-2.674	0.254	71	0.206	1358	1441	99.1672	0.193
2.674-2.858	0.22	69	0.207	1306	1383	99.4215	0.205
2.858-3.085	0.252	64	0.201	1213	1280	99.7656	0.201
3.085-3.377	0.275	59	0.229	1117	1179	99.7455	0.23
3.377-3.772	0.222	53	0.188	1021	1078	99.6289	0.199
3.772-4.348	0.315	49	0.179	918	969	99.7936	0.208
4.348-5.307	0.272	40	0.211	762	802	100	0.257
5.307-7.43	0.357	31	0.309	594	628	99.5223	0.354
7.43-37.193	0.302	20	0.263	371	391	100	0.336

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	18.8209	6.1148	7.5867	13.3275	3.3105	16.2996	-0.1272	1.1881	-0.037	-0.7352	-0.0904	0.3582	0.082	-0.5909	0.2176	0.0696	0.0082	-0.0417	0.1836	-0.0211	0.0643	-38.1255	1.8995	55.0682
2	13.1507	2.8776	10.5624	0.9236	3.8513	16.7883	0.1879	-0.1515	-0.0265	0.0335	-0.0078	-0.034	-0.002	-0.1139	-0.1802	0.0729	0.0453	-0.02	0.0453	0.0064	0.0589	-30.2436	4.3197	67.1621
3	5.8109	-1.2168	4.1762	3.1062	0.8136	11.0258	0.0217	-0.1724	0.2856	0.0981	-0.015	0.1627	-0.124	-0.1154	-0.0067	0.0716	-0.0029	-0.0059	0.0566	-0.0112	0.0815	-21.22	6.8245	78.6133
4	5.9431	-2.7403	1.7602	1.2902	-0.9702	2.3474	-0.0615	-0.0237	0.1504	0.0384	-0.0462	-0.0887	-0.028	0.2174	0.1077	0.1358	-0.0231	-0.0285	0.1847	-0.0158	0.1087	-10.0876	2.6902	89.4874
5	2.0367	1.0888	-1.4512	0.6143	-0.3839	6.1329	-0.1175	0.0704	-0.19	-0.0891	0.0427	-0.0976	-0.0822	0.1946	0.0748	0.1902	0.0242	-0.0198	0.1927	0.0032	0.1667	-4.3983	-4.2077	105.2317
6	3.5538	0.6567	5.6858	0.5189	0.3168	10.4743	-0.0824	0.1044	-0.0657	-0.1491	0.0203	-0.0846	0.0773	0.1615	0.0621	0.1167	-0.0028	-0.0154	0.091	0.0028	0.123	-2.037	-3.9396	120.4381
7	6.7282	5.625	6.6892	6.4864	5.4028	15.0331	0.0328	-0.1	-0.0731	0.0366	-0.0009	0.2228	0.0677	0.1934	-0.032	0.0056	0.0044	-0.0085	0.0181	0.0109	0.0653	3.7347	-3.0472	133.538
8	11.9465	0.5123	10.0002	8.2716	1.1316	16.2961	-0.0403	-0.4657	-0.0334	1.0802	-0.1211	0.0678	0.0185	-0.0361	0.1614	0.1878	-0.0497	-0.0069	0.1728	-0.0103	0.0661	9.7667	0.6185	148.3814
9	0.9572	-0.5499	0.1421	0.8658	1.2109	8.7863	0.1095	0.3671	-0.0608	-0.2896	-0.0951	0.0594	0.1322	0.0412	-0.0144	0.1822	-0.0355	-0.0138	0.1858	0.0013	0.1397	-30.975	-5.7583	51.103
10	3.7015	1.8756	4.406	4.2861	0.8971	13.2261	0.0117	0.0469	-0.0941	-0.1726	-0.088	-0.0112	0.2662	0.111	0.0763	0.0163	0.0063	-0.0097	0.0044	-0.0016	0.0739	-26.8711	-5.8702	65.3949
11	4.1131	-0.299	4.0392	4.7922	-0.3655	9.7767	-0.0777	-0.1038	-0.0404	0.1921	-0.109	0.0036	0.222	-0.0611	0.1867	0.0466	-0.0309	0.0069	0.0879	-0.0025	0.0841	-23.018	-4.8105	79.8643
12	8.6748	6.9072	8.6444	16.0446	8.1508	12.5046	0.2432	-0.6905	0.355	0.8631	-0.301	0.1236	0.5141	-0.3052	0.0578	0.1775	-0.0279	-0.0394	0.2862	-0.0166	0.0487	-15.3824	1.4669	92.2831
13	8.0696	-1.5376	0.1797	0.5912	-1.5315	8.0083	-0.0156	0.1252	0.6212	0.0298	0.0745	-0.0771	-0.5098	-0.2523	-0.0589	0.3649	-0.0416	-0.0878	0.4277	0.0419	0.2545	-1.3891	3.6342	104.7714
14	2.2841	0.2204	3.3239	0.2453	1.1705	8.1236	0.0455	0.2062	-0.0148	-0.0438	-0.0451	0.0081	-0.0277	0.0108	-0.0004	0.1523	-0.0071	-0.0061	0.1588	0.0144	0.1366	7.2989	-1.5723	115.5853
15	2.3432	0.0091	2.5557	1.2758	1.5253	12.7585	0.0283	0.1279	0.138	-0.1631	-0.0004	-0.0777	-0.1869	0.0539	-0.0279	0.0335	0.0064	-0.0113	0.0155	-0.0041	0.0845	13.5209	-2.8135	128.7025
16	0.7677	-0.8355	0.0114	1.7336	1.2571	11.7065	-0.0335	-0.2239	0.0376	0.3067	0.0109	-0.079	0.1	0.2394	0.0226	0.1493	-0.0595	-0.0211	0.1847	0.0119	0.1092	17.7594	-5.7971	144.3106
17	14.5255	-3.5049	8.9045	7.035	-5.0123	10.2915	-0.3042	1.3236	-0.0814	-0.8413	0.278	0.3235	-0.7519	-0.0398	0.0261	0.4253	0.0395	-0.0838	0.3678	0.0344	0.2035	-28.3978	4.9769	50.3925
18	13.4167	-0.6446	8.4108	3.1512	-1.1061	14.0404	-0.0653	0.5058	0.7563	-0.3104	-0.0862	-0.0383	-0.5276	0.2326	0.1514	0.0712	0.0138	0.0072	0.0296	0.018	0.088	-20.6392	2.695	62.1642
19	5.5886	-0.8132	4.1176	1.4505	-1.1965	10.5448	0.0193	-0.0278	0.0854	-0.009	0.0005	-0.138	-0.0204	0.1945	-0.0198	0.0277	-0.0002	-0.0076	0.0679	-0.0258	0.0913	-13.1726	-0.7098	74.8805
20	1.2234	0.7841	-2.4397	0.5924	-1.9543	8.0905	0.0036	-0.1419	-0.0771	0.0183	-0.0558	-0.0102	0.4052	0.1384	0.0522	0.1775	0.0072	-0.011	0.1688	-0.0277	0.1196	-11.7902	-3.1212	90.3329
21	8.3093	2.1913	2.5164	14.3206	3.1349	5.0196	0.0549	0.2226	-0.0123	-0.2969	0.0749	-0.4472	-0.4482	-0.3804	-0.1298	0.3045	0.041	-0.0658	0.2898	0.043	0.136	-8.4252	2.5458	107.3977
22	1.4994	0.2248	2.9677	0.0748	0.4193	8.8783	-0.0093	0.2884	0.1046	-0.0627	0.0585	0.0116	0.046	-0.0538	-0.0492	0.1438	-0.0084	-0.0549	0.2011	0.0309	0.1726	-0.1544	6.1157	119.8234
23	10.5335	-0.9742	8.4841	5.0564	-4.158	16.1845	-0.0351	-0.1976	-0.1279	0.1348	0.2924	0.3183	-0.2354	-0.4933	-0.2573	0.0236	0.0139	-0.0204	0.0226	0.0128	0.0643	8.317	6.2236	131.6612
24	5.9317	-1.2765	6.153	0.3054	-1.3442	6.4697	-0.0309	-0.1189	0.0946	0.0545	-0.0308	-0.0621	-0.0081	0.0192	0.0617	0.1588	-0.0113	-0.0633	0.257	-0.0197	0.1706	20.7464	5.0658	144.9082

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Label asym-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	281 - 290
2	X-RAY DIFFRACTION	2	ALL	A	291 - 300
3	X-RAY DIFFRACTION	3	ALL	A	301 - 310
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11	X-RAY DIFFRACTION	11	ALL	B	301 - 310
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