PDB-2gnx: X-ray structure of a hypothetical protein from Mouse Mm.209172

ID or keywords:

Entry

Database: PDB / ID: 2gnx

Title

X-ray structure of a hypothetical protein from Mouse Mm.209172

Components

hypothetical protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION /

PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG

Function / homology

Function and homology information

KICSTOR complex / Amino acids regulate mTORC1 / protein localization to lysosome /

intercellular bridge / cellular response to glucose starvation / negative regulation of TORC1 signaling / cellular response to amino acid starvation /

lysosome / lysosomal membrane
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.45 Å

Authors

Phillips Jr., G.N. / McCoy, J.G. / Bitto, E. / Wesenberg, G.E. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: To be Published
Title: X-ray structure of a hypothetical protein from Mouse Mm.209172
Authors: Phillips Jr., G.N. / McCoy, J.G. / Bitto, E. / Wesenberg, G.E. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)

History

Deposition	Apr 11, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 2, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software

Remark 999

SEQUENCE 22 residues of the N-terminal domain of the protein (residues 1-122) have been modeled as ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2gnx.cif.gz	70.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2gnx.ent.gz	53.4 KB	Display	PDB format
PDBx/mmJSON format	2gnx.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/gn/2gnx ftp://data.pdbj.org/pub/pdb/validation_reports/gn/2gnx	HTTPS FTP

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Related structure data

Similar structure data	4qdg-1 16vp-d 5v7w-d 5cq9-2 4qjd-1 5juw-d 4iod-5 5iwd-d 4qo1-d 6eeb-2 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: GO.34351

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: hypothetical protein

39.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	82.687, 198.962, 67.076
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	hypothetical protein / Mass: 39353.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mm209172, BC065058 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 P(RARE2) / References: GenBank: 41055590, UniProt: Q6P1I3*PLUS
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.72 Å³/Da / Density % sol: 54.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 MES PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (0.003 SODIUM CHLORIDE, 0.10 M ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 MES PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (0.003 SODIUM CHLORIDE, 0.10 M HEPES PH 7.5) Crystals cryo-protected with Fomblin followed by Paratone N, vapor diffusion, hanging drop, temperature 293K

Crystal

Density Matthews: 2.72 Å³/Da / Density % sol: 54.81 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 MES PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (0.003 SODIUM CHLORIDE, 0.10 M ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 0.97182 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 10, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR

Radiation

Monochromator: CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97182 Å / Relative weight: 1

Reflection

Resolution: 2.45→40.966 Å / Num. obs: 35469 / % possible obs: 91.8 % / Redundancy: 9.4 % / R_merge(I) obs: 0.07 / Χ²: 1.292 / Net I/σ(I): 12.896

Reflection shell

Resolution: 2.45→2.54 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.682 / Mean I/σ(I) obs: 1.697 / Num. unique all: 1473 / Χ²: 0.913 / % possible all: 71.4

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Phasing

Phasing

Method:

SAD

Phasing MAD set

Highest resolution: 2.45 Å / Lowest resolution: 40.97 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	17121	1758
ISO_2	0.902	0.887	0.409	0.354	14947	1607
ISO_3	0.828	0.727	1.513	1.513	16906	1743
ANO_1	0.545	0	1.876	0	16552	0
ANO_2	0.733	0	0.659	0	15172	0
ANO_3	0.613	0	1.781	0	16577	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	10.6-40.97	0	0	0	0	149	75
ISO_1	7.63-10.6	0	0	0	0	304	85
ISO_1	6.26-7.63	0	0	0	0	441	93
ISO_1	5.44-6.26	0	0	0	0	530	88
ISO_1	4.87-5.44	0	0	0	0	614	87
ISO_1	4.45-4.87	0	0	0	0	685	88
ISO_1	4.13-4.45	0	0	0	0	746	88
ISO_1	3.86-4.13	0	0	0	0	807	94
ISO_1	3.64-3.86	0	0	0	0	877	91
ISO_1	3.46-3.64	0	0	0	0	911	92
ISO_1	3.3-3.46	0	0	0	0	975	93
ISO_1	3.16-3.3	0	0	0	0	1023	77
ISO_1	3.04-3.16	0	0	0	0	1066	96
ISO_1	2.93-3.04	0	0	0	0	1118	92
ISO_1	2.83-2.93	0	0	0	0	1134	101
ISO_1	2.74-2.83	0	0	0	0	1205	92
ISO_1	2.66-2.74	0	0	0	0	1197	91
ISO_1	2.58-2.66	0	0	0	0	1216	93
ISO_1	2.51-2.58	0	0	0	0	1158	80
ISO_1	2.45-2.51	0	0	0	0	965	62
ANO_1	10.6-40.97	0.49	0	2.021	0	133	0
ANO_1	7.63-10.6	0.396	0	2.684	0	297	0
ANO_1	6.26-7.63	0.328	0	3.409	0	440	0
ANO_1	5.44-6.26	0.319	0	3.517	0	524	0
ANO_1	4.87-5.44	0.371	0	3.052	0	608	0
ANO_1	4.45-4.87	0.452	0	2.549	0	681	0
ANO_1	4.13-4.45	0.471	0	2.394	0	741	0
ANO_1	3.86-4.13	0.511	0	2.136	0	804	0
ANO_1	3.64-3.86	0.541	0	2.051	0	875	0
ANO_1	3.46-3.64	0.607	0	1.858	0	908	0
ANO_1	3.3-3.46	0.609	0	1.628	0	968	0
ANO_1	3.16-3.3	0.652	0	1.482	0	1021	0
ANO_1	3.04-3.16	0.718	0	1.217	0	1065	0
ANO_1	2.93-3.04	0.8	0	0.952	0	1111	0
ANO_1	2.83-2.93	0.861	0	0.781	0	1131	0
ANO_1	2.74-2.83	0.926	0	0.598	0	1199	0
ANO_1	2.66-2.74	0.961	0	0.471	0	1182	0
ANO_1	2.58-2.66	0.975	0	0.401	0	1141	0
ANO_1	2.51-2.58	0.99	0	0.333	0	1005	0
ANO_1	2.45-2.51	1	0	0.323	0	718	0
ISO_2	10.6-40.97	0.895	0.902	0.487	0.37	148	74
ISO_2	7.63-10.6	0.847	0.777	0.542	0.455	304	85
ISO_2	6.26-7.63	0.836	0.801	0.543	0.462	441	93
ISO_2	5.44-6.26	0.839	0.834	0.51	0.367	530	88
ISO_2	4.87-5.44	0.883	0.828	0.426	0.38	614	87
ISO_2	4.45-4.87	0.912	0.928	0.374	0.286	685	88
ISO_2	4.13-4.45	0.925	0.888	0.342	0.286	746	88
ISO_2	3.86-4.13	0.91	0.934	0.343	0.28	807	94
ISO_2	3.64-3.86	0.928	0.888	0.318	0.275	877	91
ISO_2	3.46-3.64	0.913	0.951	0.289	0.241	911	92
ISO_2	3.3-3.46	0.939	0.938	0.306	0.247	975	93
ISO_2	3.16-3.3	0.941	0.92	0.297	0.229	1023	77
ISO_2	3.04-3.16	0.959	0.959	0.303	0.25	1066	96
ISO_2	2.93-3.04	0.97	0.995	0.299	0.21	1117	92
ISO_2	2.83-2.93	0.948	1.022	0.281	0.196	1134	101
ISO_2	2.74-2.83	0.95	1.032	0.243	0.152	1203	92
ISO_2	2.66-2.74	0.945	1.033	0.17	0.143	1162	90
ISO_2	2.58-2.66	0.954	0.968	0.156	0.121	1096	82
ISO_2	2.51-2.58	0.9	1.089	0.127	0.059	108	4
ISO_2	2.45-2.51	0	0	0	0	0	0
ANO_2	10.6-40.97	0.78	0	0.578	0	167	0
ANO_2	7.63-10.6	0.691	0	0.711	0	335	0
ANO_2	6.26-7.63	0.647	0	0.791	0	464	0
ANO_2	5.44-6.26	0.639	0	0.828	0	556	0
ANO_2	4.87-5.44	0.649	0	0.832	0	636	0
ANO_2	4.45-4.87	0.664	0	0.83	0	710	0
ANO_2	4.13-4.45	0.681	0	0.797	0	775	0
ANO_2	3.86-4.13	0.69	0	0.773	0	839	0
ANO_2	3.64-3.86	0.717	0	0.754	0	903	0
ANO_2	3.46-3.64	0.754	0	0.703	0	940	0
ANO_2	3.3-3.46	0.785	0	0.594	0	1006	0
ANO_2	3.16-3.3	0.814	0	0.545	0	1050	0
ANO_2	3.04-3.16	0.869	0	0.448	0	1094	0
ANO_2	2.93-3.04	0.926	0	0.342	0	1152	0
ANO_2	2.83-2.93	0.953	0	0.275	0	1168	0
ANO_2	2.74-2.83	0.972	0	0.222	0	1214	0
ANO_2	2.66-2.74	0.987	0	0.167	0	1104	0
ANO_2	2.58-2.66	0.996	0	0.147	0	969	0
ANO_2	2.51-2.58	0.995	0	0.131	0	90	0
ANO_2	2.45-2.51	0	0	0	0	0	0
ISO_3	10.6-40.97	0.738	0.591	1.605	1.845	143	73
ISO_3	7.63-10.6	0.859	0.673	1.971	2.162	304	85
ISO_3	6.26-7.63	0.555	0.395	3.409	3.486	441	93
ISO_3	5.44-6.26	0.537	0.694	3.631	2.387	530	88
ISO_3	4.87-5.44	0.778	0.644	2.461	2.077	614	87
ISO_3	4.45-4.87	0.897	0.835	2.065	1.618	684	88
ISO_3	4.13-4.45	0.973	0.745	1.909	1.709	746	88
ISO_3	3.86-4.13	1.048	0.93	1.769	1.407	807	94
ISO_3	3.64-3.86	1.091	0.788	1.62	1.348	877	91
ISO_3	3.46-3.64	1.105	0.953	1.378	1.063	910	92
ISO_3	3.3-3.46	0.949	0.956	1.497	1.185	975	93
ISO_3	3.16-3.3	0.796	0.704	1.44	0.966	1022	77
ISO_3	3.04-3.16	0.756	0.798	1.137	0.708	1066	95
ISO_3	2.93-3.04	0.747	0.742	0.931	0.541	1117	92
ISO_3	2.83-2.93	0.742	0.883	0.712	0.448	1132	100
ISO_3	2.74-2.83	0.756	0.878	0.56	0.342	1202	92
ISO_3	2.66-2.74	0.845	0.889	0.411	0.28	1192	91
ISO_3	2.58-2.66	0.851	0.824	0.316	0.239	1197	93
ISO_3	2.51-2.58	0.868	0.945	0.244	0.175	1096	77
ISO_3	2.45-2.51	0.98	0.978	0.185	0.129	851	54
ANO_3	10.6-40.97	0.513	0	2.069	0	130	0
ANO_3	7.63-10.6	0.4	0	2.974	0	298	0
ANO_3	6.26-7.63	0.303	0	4.286	0	440	0
ANO_3	5.44-6.26	0.293	0	4.401	0	524	0
ANO_3	4.87-5.44	0.374	0	3.42	0	607	0
ANO_3	4.45-4.87	0.491	0	2.641	0	681	0
ANO_3	4.13-4.45	0.506	0	2.435	0	740	0
ANO_3	3.86-4.13	0.542	0	2.29	0	804	0
ANO_3	3.64-3.86	0.589	0	2.078	0	875	0
ANO_3	3.46-3.64	0.681	0	1.775	0	908	0
ANO_3	3.3-3.46	0.667	0	1.635	0	969	0
ANO_3	3.16-3.3	0.705	0	1.407	0	1021	0
ANO_3	3.04-3.16	0.798	0	1.057	0	1064	0
ANO_3	2.93-3.04	0.859	0	0.859	0	1112	0
ANO_3	2.83-2.93	0.908	0	0.681	0	1130	0
ANO_3	2.74-2.83	0.95	0	0.512	0	1198	0
ANO_3	2.66-2.74	0.97	0	0.39	0	1181	0
ANO_3	2.58-2.66	0.984	0	0.355	0	1143	0
ANO_3	2.51-2.58	0.99	0	0.28	0	1031	0
ANO_3	2.45-2.51	0.999	0	0.264	0	721	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	9.216	-0.535	3.568	SE	62.88	1.43
2	8.682	-34.531	-0.149	SE	66.35	1.38
3	-24.324	-84.233	1.389	SE	74.36	1.44
4	36.389	-73.982	6.935	SE	89.77	1.47
5	-0.074	-46.729	0.332	SE	80.88	1.08
6	57.021	-54.867	3.025	SE	97.33	1.51
7	21.598	-5.035	2.727	SE	103.65	1.33
8	63.364	-37.699	4.732	SE	108.82	1.06

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 20103

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.71-100	85	0.644	503
6.87-8.71	51.3	0.875	507
5.97-6.87	44.9	0.922	513
5.42-5.97	43.5	0.942	503
5.02-5.42	35	0.946	504
4.7-5.02	36.5	0.942	536
4.43-4.7	39	0.941	574
4.2-4.43	38.8	0.938	610
4-4.2	43.2	0.92	647
3.83-4	42.4	0.925	660
3.68-3.83	42.8	0.915	701
3.55-3.68	46.6	0.907	715
3.43-3.55	47.9	0.894	736
3.32-3.43	49	0.882	769
3.22-3.32	51	0.868	805
3.13-3.22	53.2	0.834	804
3.05-3.13	56.7	0.806	829
2.97-3.05	58.6	0.807	857
2.9-2.97	63.8	0.779	892
2.83-2.9	67.3	0.758	888
2.77-2.83	68.8	0.733	915
2.71-2.77	69.5	0.729	937
2.66-2.71	78.7	0.715	910
2.6-2.66	79.7	0.701	938
2.56-2.6	82	0.706	913
2.51-2.56	83	0.698	872
2.45-2.51	88.2	0.64	1065

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
CNS	1.1	refinement
PDB_EXTRACT	1.701	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 2.45→40.97 Å / R_factor R_free error: 0.008 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.322	1772	5 %	Random
R_work	0.281	-	-	-
all	-	39313	-	-
obs	-	35469	90.2 %	-

Solvent computation

Solvent model: CNS bulk solvent model used / B_sol: 57.8555 Å² / k_sol: 0.316349 e/Å³

Displacement parameters

B_iso max: 142.01 Å² / B_iso mean: 76.74 Å² / B_iso min: 34.58 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	9.5 Å²	0 Å²	0 Å²
2-	-	-7.91 Å²	0 Å²
3-	-	-	-1.59 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.47 Å	0.42 Å
Luzzati d res low	-	5 Å
Luzzati sigma a	0.37 Å	0.4 Å
Luzzati d res high	-	2.45

Refinement step

Cycle: LAST / Resolution: 2.45→40.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2290	0	0	25	2315

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	x_bond_d	0.008
X-RAY DIFFRACTION	x_angle_deg	1.2
X-RAY DIFFRACTION	x_torsion_deg	21.4
X-RAY DIFFRACTION	x_torsion_impr_deg	0.72

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	% reflection R_free (%)	R_factor R_work	Num. reflection R_work	R_factor R_free error	Num. reflection all	Num. reflection obs	% reflection obs (%)
2.45-2.56	0.448	106	3.4	0.416	3045	0.044	4927	3151	64
2.56-2.7	0.375	216	4.9	0.388	4168	0.026	4929	4384	88.9
2.7-2.87	0.43	242	5.1	0.355	4462	0.028	4899	4704	96
2.87-3.09	0.328	236	5	0.313	4491	0.021	4927	4727	95.9
3.09-3.4	0.337	264	5.6	0.283	4434	0.021	4881	4698	96.3
3.4-3.89	0.321	250	5.3	0.277	4475	0.02	4931	4725	95.8
3.89-4.9	0.278	260	5.6	0.234	4414	0.017	4929	4674	94.8
4.9-40.97	0.327	198	4.5	0.284	4208	0.023	4918	4406	89.6

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Movie

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Links

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Experimental details

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Experiment

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About Yorodumi

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi