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

ID or keywords:

Entry

Database: PDB / ID: 7oad

Title

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

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 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 II
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	7oad.cif.gz	201.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7oad.ent.gz	161 KB	Display	PDB format
PDBx/mmJSON format	7oad.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7oad_validation.pdf.gz	440 KB	Display	wwPDB validaton report
Full document	7oad_full_validation.pdf.gz	440.4 KB	Display
Data in XML	7oad_validation.xml.gz	9.5 KB	Display
Data in CIF	7oad_validation.cif.gz	12.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oa/7oad ftp://data.pdbj.org/pub/pdb/validation_reports/oa/7oad	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)	36.351, 38.561, 99.254
Angle α, β, γ (deg.)	90.000, 98.877, 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 - 361 / Label seq-ID: 5 - 84

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: 2.28 Å³/Da / Density % sol: 45.96 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1M tri-sodium citrate pH 4.5, 7.1% 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→49.03 Å / Num. obs: 18659 / % possible obs: 99.7 % / Redundancy: 6.71 % / CC_1/2: 1 / R_merge(I) obs: 0.047 / Net I/σ(I): 19.67
Reflection shell	Resolution: 2→2.12 Å / Redundancy: 6.63 % / R_merge(I) obs: 0.753 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 2993 / CC_1/2: 0.95 / % possible all: 99.7

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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→49.03 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.926 / SU B: 18.818 / SU ML: 0.213 / Cross valid method: FREE R-VALUE / ESU R: 0.236 / ESU R Free: 0.202
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2939	933	-
R_work	0.2535	17724	-
all	0.256	-	-
obs	-	18657	99.711 %

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: 75.374 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.155 Å²	0 Å²	7.131 Å²
2-	-	-0.534 Å²	-0 Å²
3-	-	-	0.44 Å²

Refinement step

Cycle: LAST / Resolution: 2→49.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2007	0	0	7	2014

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	2028
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	2103
X-RAY DIFFRACTION	r_angle_refined_deg	1.368	1.967	2703
X-RAY DIFFRACTION	r_angle_other_deg	1.076	3	4869
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.874	5	237
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.042	26.452	93
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.475	15	471
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.273	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	306
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2169
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	405
X-RAY DIFFRACTION	r_nbd_refined	0.233	0.2	479
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.145	0.2	1891
X-RAY DIFFRACTION	r_nbtor_refined	0.191	0.2	955
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1166
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.112	0.2	18
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.201	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.206	0.2	71
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.219	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.775	3.309	957
X-RAY DIFFRACTION	r_mcbond_other	1.77	3.308	956
X-RAY DIFFRACTION	r_mcangle_it	2.536	4.955	1191
X-RAY DIFFRACTION	r_mcangle_other	2.537	4.957	1192
X-RAY DIFFRACTION	r_scbond_it	2.91	3.755	1071
X-RAY DIFFRACTION	r_scbond_other	2.908	3.757	1072
X-RAY DIFFRACTION	r_scangle_it	4.513	5.471	1512
X-RAY DIFFRACTION	r_scangle_other	4.511	5.474	1513
X-RAY DIFFRACTION	r_lrange_it	5.745	26.179	2344
X-RAY DIFFRACTION	r_lrange_other	5.743	26.084	2339
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.12	0.05	4259
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.1	0.05	4330
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.12	0.05	4235

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	4259	0.12
1	2	B	4259	0.12
2	1	A	4330	0.1
2	2	C	4330	0.1
3	1	B	4235	0.12
3	2	C	4235	0.12

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
2-2.052	0.389	69	0.401	1310	1379	100	0.357
2.052-2.108	0.373	67	0.374	1262	1331	99.8497	0.337
2.108-2.169	0.362	64	0.336	1221	1286	99.9222	0.312
2.169-2.236	0.317	63	0.295	1192	1255	100	0.262
2.236-2.309	0.264	61	0.271	1174	1235	100	0.235
2.309-2.39	0.293	59	0.265	1121	1182	99.8308	0.233
2.39-2.48	0.34	57	0.266	1068	1125	100	0.237
2.48-2.581	0.294	56	0.253	1071	1127	100	0.224
2.581-2.695	0.231	51	0.238	980	1031	100	0.216
2.695-2.826	0.373	52	0.268	970	1023	99.9023	0.25
2.826-2.978	0.324	48	0.234	914	964	99.7925	0.218
2.978-3.158	0.286	46	0.265	873	920	99.8913	0.254
3.158-3.375	0.309	42	0.297	807	849	100	0.284
3.375-3.644	0.284	41	0.244	768	809	100	0.255
3.644-3.99	0.353	37	0.234	707	746	99.7319	0.252
3.99-4.457	0.219	33	0.202	638	672	99.8512	0.236
4.457-5.14	0.295	30	0.191	568	600	99.6667	0.235
5.14-6.278	0.325	26	0.292	490	517	99.8066	0.351
6.278-8.806	0.227	20	0.246	382	405	99.2593	0.328
8.806-49.033	0.246	11	0.29	199	245	85.7143	0.444

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	6.8318	-3.045	-2.2728	7.7552	1.3785	10.137	-0.0776	1.1514	-0.3104	-1.0189	-0.4127	-0.7821	0.0087	0.3171	0.4903	0.6566	-0.0548	0.0086	0.5596	0.0084	0.6085	39.6244	0.1816	-11.6804
2	7.4894	0.6909	-4.6902	7.3463	-0.6638	5.9366	-0.1655	0.5092	-0.3241	-0.4235	0.0673	0.2328	0.0434	-0.4979	0.0982	0.41	-0.0143	-0.103	0.3031	-0.0369	0.3734	29.398	0.0527	-0.5681
3	9.8128	3.564	-7.7513	7.9632	-0.6114	10.5188	0.1592	0.3971	-0.1969	0.0298	-0.0589	0.332	-0.3019	-0.4209	-0.1002	0.3922	0.0087	-0.0428	0.4053	-0.012	0.4501	19.3491	0.0048	10.1332
4	14.4562	-2.1072	-12.2575	0.3292	1.7897	10.3981	0.338	0.1569	0.2362	-0.0022	-0.1138	0.0208	-0.312	-0.1747	-0.2241	0.5052	-0.0432	0.0322	0.5533	0.0205	0.5929	8.4973	-0.028	21.5028
5	14.3954	-0.8152	-8.1335	2.4606	-0.1136	11.2375	-0.3513	0.1338	-0.6057	-0.7226	-0.1831	-0.6526	0.155	1.0751	0.5344	0.3896	0.017	0.0511	0.2383	0.0325	0.4336	-1.49	0.0439	31.7676
6	8.0437	2.0978	-6.0909	2.0378	-0.2617	8.446	0.0007	-0.3504	-0.4122	-0.3168	-0.1227	-0.2912	-0.1429	0.5693	0.122	0.2536	0.0332	-0.1819	0.0579	0.0073	0.3136	-11.6912	0.1322	42.4867
7	8.3961	-0.1802	-4.4577	5.0808	-0.6442	5.819	0.1445	-0.5045	0.1217	0.2379	-0.1224	-0.109	-0.0867	0.5677	-0.0221	0.184	-0.0249	-0.1479	0.0606	-0.0051	0.1974	-21.82	0.341	52.9649
8	12.4116	-2.0944	-5.584	11.5446	1.8697	11.4537	-0.042	-1.3429	0.0608	1.1979	0.1469	0.6414	-0.2547	0.1751	-0.1048	0.3929	-0.0382	-0.0592	0.1799	0.0008	0.2703	-31.1404	0.3851	63.0003

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Label asym-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	281 - 292
2	X-RAY DIFFRACTION	1	ALL	B	281 - 292
3	X-RAY DIFFRACTION	1	ALL	C	281 - 292
4	X-RAY DIFFRACTION	2	ALL	A	293 - 302
5	X-RAY DIFFRACTION	2	ALL	B	293 - 302
6	X-RAY DIFFRACTION	2	ALL	C	293 - 302
7	X-RAY DIFFRACTION	3	ALL	A	303 - 312
8	X-RAY DIFFRACTION	3	ALL	B	303 - 312
9	X-RAY DIFFRACTION	3	ALL	C	303 - 312
10	X-RAY DIFFRACTION	4	ALL	A	313 - 322
11	X-RAY DIFFRACTION	4	ALL	B	313 - 322
12	X-RAY DIFFRACTION	4	ALL	C	313 - 322
13	X-RAY DIFFRACTION	5	ALL	A	323 - 332
14	X-RAY DIFFRACTION	5	ALL	B	323 - 332
15	X-RAY DIFFRACTION	5	ALL	C	323 - 332
16	X-RAY DIFFRACTION	6	ALL	A	333 - 342
17	X-RAY DIFFRACTION	6	ALL	B	333 - 342
18	X-RAY DIFFRACTION	6	ALL	C	333 - 342
19	X-RAY DIFFRACTION	7	ALL	A	343 - 352
20	X-RAY DIFFRACTION	7	ALL	B	343 - 352
21	X-RAY DIFFRACTION	7	ALL	C	343 - 352
22	X-RAY DIFFRACTION	8	ALL	A	353 - 363
23	X-RAY DIFFRACTION	8	ALL	B	353 - 363
24	X-RAY DIFFRACTION	8	ALL	C	353 - 363

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