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

ID or keywords:

Entry

Database: PDB / ID: 7oac

Title

conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors, mutant beta1/A, crystal form I

Components

General control transcription factor GCN4,conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors, mutant beta1/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: 2.15 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 beta1/A, crystal form I
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	7oac.cif.gz	199.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7oac.ent.gz	158.4 KB	Display	PDB format
PDBx/mmJSON format	7oac.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7oac_validation.pdf.gz	439.5 KB	Display	wwPDB validaton report
Full document	7oac_full_validation.pdf.gz	440.1 KB	Display
Data in XML	7oac_validation.xml.gz	9.5 KB	Display
Data in CIF	7oac_validation.cif.gz	12.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oa/7oac ftp://data.pdbj.org/pub/pdb/validation_reports/oa/7oac	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 beta1/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 beta1/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 beta1/A,General control transcription factor GCN4

30.2 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)	36.811, 37.365, 90.232
Angle α, β, γ (deg.)	90.000, 98.981, 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: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 282 - 362 / Label seq-ID: 5 - 85

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	B	B
2	3	C	C

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 beta1/A,General control transcription factor GCN4 / Amino acid biosynthesis regulatory protein / General control protein GCN4 Mass: 10065.771 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

General control transcription factor GCN4,conserved hypothetical protein residues 311-335 from Candidatus Magnetomorum sp. HK-1 fused to GCN4 adaptors, mutant beta1/A,General control transcription factor GCN4 / Amino acid biosynthesis regulatory protein / General control protein GCN4

Mass: 10065.771 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: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.03 Å³/Da / Density % sol: 39.4 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.1M tri-sodium citrate pH 4.5, 7.1 % (w/v) PEG 10000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 15, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9998 Å / Relative weight: 1
Reflection	Resolution: 2.15→34.46 Å / Num. obs: 13455 / % possible obs: 99.7 % / Redundancy: 6.61 % / CC_1/2: 1 / R_merge(I) obs: 0.072 / Net I/σ(I): 13.37
Reflection shell	Resolution: 2.15→2.28 Å / Redundancy: 6.78 % / R_merge(I) obs: 1.128 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 2156 / CC_1/2: 0.7 / % possible all: 99.9

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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: 2.15→34.459 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.946 / SU B: 24.489 / SU ML: 0.261 / Cross valid method: FREE R-VALUE / ESU R: 0.344 / ESU R Free: 0.225
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2576	673	-
R_work	0.2366	12781	-
all	0.238	-	-
obs	-	13454	99.755 %

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: 60.836 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.614 Å²	-0 Å²	-4.382 Å²
2-	-	-0.931 Å²	-0 Å²
3-	-	-	4.696 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→34.459 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2034	0	0	7	2041

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	2055
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	2142
X-RAY DIFFRACTION	r_angle_refined_deg	1.417	1.969	2736
X-RAY DIFFRACTION	r_angle_other_deg	1.196	3	4962
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.711	5	240
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	43.786	26.452	93
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.423	15	483
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.097	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	309
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2190
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	408
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	411
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.164	0.2	1714
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	927
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.071	0.2	1124
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.205	0.2	17
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.155	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.292	0.2	90
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.297	0.2	4
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.017	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	3.876	4.369	969
X-RAY DIFFRACTION	r_mcbond_other	3.877	4.366	968
X-RAY DIFFRACTION	r_mcangle_it	5.32	6.54	1206
X-RAY DIFFRACTION	r_mcangle_other	5.318	6.543	1207
X-RAY DIFFRACTION	r_scbond_it	5.469	5.28	1086
X-RAY DIFFRACTION	r_scbond_other	5.467	5.283	1087
X-RAY DIFFRACTION	r_scangle_it	8.654	7.565	1530
X-RAY DIFFRACTION	r_scangle_other	8.651	7.568	1531
X-RAY DIFFRACTION	r_lrange_it	10.442	34.461	2283
X-RAY DIFFRACTION	r_lrange_other	10.43	34.431	2278
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.12	0.05	4253
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.107	0.05	4276
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.126	0.05	4224

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	4253	0.12
1	2	B	4253	0.12
2	1	A	4276	0.11
2	2	C	4276	0.11
3	1	B	4224	0.13
3	2	C	4224	0.13

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
2.15-2.205	0.364	49	0.421	928	980	99.6939	0.398
2.205-2.266	0.442	48	0.406	921	969	100	0.372
2.266-2.331	0.358	47	0.354	884	931	100	0.316
2.331-2.402	0.373	44	0.322	837	881	100	0.276
2.402-2.481	0.232	45	0.343	868	913	100	0.297
2.481-2.567	0.238	42	0.29	782	824	100	0.254
2.567-2.664	0.336	42	0.261	805	848	99.8821	0.234
2.664-2.772	0.313	39	0.25	734	773	100	0.223
2.772-2.894	0.242	38	0.241	731	769	100	0.222
2.894-3.034	0.342	36	0.251	686	722	100	0.234
3.034-3.197	0.29	35	0.259	659	694	100	0.247
3.197-3.389	0.318	33	0.256	624	657	100	0.246
3.389-3.621	0.292	31	0.219	596	627	100	0.221
3.621-3.907	0.268	29	0.202	541	573	99.4764	0.206
3.907-4.275	0.177	26	0.18	506	532	100	0.2
4.275-4.77	0.121	25	0.165	472	498	99.7992	0.198
4.77-5.49	0.33	22	0.215	408	433	99.3072	0.255
5.49-6.682	0.271	18	0.276	354	372	100	0.312
6.682-9.277	0.167	15	0.197	290	305	100	0.268
9.277-34.459	0.318	9	0.24	155	182	90.1099	0.324

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	2.7769	0.4088	1.2693	3.6626	-0.1301	3.3413	0.1961	0.2092	0.1421	-0.2157	-0.0341	0.3072	0.2658	-0.0308	-0.162	0.0723	0.0225	0.0035	0.1456	0.0354	0.064	-42.0538	-0.0372	-11.7293
2	4.5866	-0.2847	3.1269	0.9127	-0.3746	2.1696	0.1208	-0.0304	-0.0392	0.0133	-0.0894	-0.0153	0.0789	-0.0174	-0.0314	0.1273	0.0198	0.0628	0.138	0.0037	0.035	-31.606	-0.0244	-2.2678
3	3.9759	-0.2567	2.5342	0.2295	-0.4809	2.1486	-0.0431	-0.1213	0.2045	-0.0915	-0.0503	-0.0208	0.1293	-0.0362	0.0933	0.1206	-0.0047	0.0341	0.0605	0.0108	0.0672	-20.3932	-0.0303	7.0162
4	4.8161	-0.7145	2.143	0.4857	-1.0866	2.5414	-0.056	-0.0381	0.1721	0.0123	-0.0144	-0.0227	-0.0464	-0.034	0.0704	0.1272	-0.0112	0.0293	0.087	-0.0204	0.0369	-9.0078	-0.078	15.9489
5	4.5737	0.4538	3.6765	0.0556	0.415	3.295	-0.0198	0.0422	0.1876	0.022	-0.0673	0.0131	0.2185	-0.1656	0.0871	0.1727	-0.0826	-0.0013	0.1662	0.0264	0.0442	3.0827	0.29	26.2464
6	3.4132	0.7451	3.3013	0.2845	0.8258	3.3305	0.1127	-0.0631	0.1137	0.0108	-0.0984	-0.0618	0.152	-0.0742	-0.0143	0.1002	0.0055	0.0355	0.0836	-0.0011	0.1036	13.0851	0.4675	35.6734
7	3.3418	0.2512	2.8926	0.0854	0.1869	2.5183	0.276	-0.0748	-0.1035	0.0661	-0.1353	0.0342	0.2379	-0.0208	-0.1407	0.1753	-0.0353	0.0524	0.1642	-0.05	0.0416	23.4554	0.3162	46.0653
8	1.9124	-1.9158	0.6621	1.9569	-0.5525	3.1768	-0.0041	0.0553	0.0019	0.0876	-0.0681	0.0047	-0.0147	0.1487	0.0721	0.1767	-0.0634	0.0099	0.0875	0.0127	0.007	35.1749	0.0327	58.1347

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	1	ALL	B	281 - 290
3	X-RAY DIFFRACTION	1	ALL	C	281 - 290
4	X-RAY DIFFRACTION	2	ALL	A	291 - 300
5	X-RAY DIFFRACTION	2	ALL	B	291 - 300
6	X-RAY DIFFRACTION	2	ALL	C	291 - 300
7	X-RAY DIFFRACTION	3	ALL	A	301 - 310
8	X-RAY DIFFRACTION	3	ALL	B	301 - 310
9	X-RAY DIFFRACTION	3	ALL	C	301 - 310
10	X-RAY DIFFRACTION	4	ALL	A	311 - 320
11	X-RAY DIFFRACTION	4	ALL	B	311 - 320
12	X-RAY DIFFRACTION	4	ALL	C	311 - 320
13	X-RAY DIFFRACTION	5	ALL	A	321 - 330
14	X-RAY DIFFRACTION	5	ALL	B	321 - 330
15	X-RAY DIFFRACTION	5	ALL	C	321 - 330
16	X-RAY DIFFRACTION	6	ALL	A	331 - 340
17	X-RAY DIFFRACTION	6	ALL	B	331 - 340
18	X-RAY DIFFRACTION	6	ALL	C	331 - 340
19	X-RAY DIFFRACTION	7	ALL	A	341 - 350
20	X-RAY DIFFRACTION	7	ALL	B	341 - 350
21	X-RAY DIFFRACTION	7	ALL	C	341 - 350
22	X-RAY DIFFRACTION	8	ALL	A	351 - 363
23	X-RAY DIFFRACTION	8	ALL	B	351 - 363
24	X-RAY DIFFRACTION	8	ALL	C	351 - 363

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