PDB-2gm3: Crystal Structure of an Universal Stress Protein Family Protein f...

ID or keywords:

Entry

Database: PDB / ID: 2gm3

Title

Crystal Structure of an Universal Stress Protein Family Protein from Arabidopsis Thaliana At3g01520 with AMP Bound

Components

unknown protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / At3g01520 / putative ethylene-responsive protein / USP Domain / nucleotide binding domain / AMP /

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

Function / homology

Function and homology information

AMP binding /

plasma membrane /

cytosol
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.461 Å

Authors

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

Citation

Journal: Proteins / Year: 2015
Title: Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from arabidopsis thaliana in complex with AMP.
Authors: Kim, D.O.J. / Bitto, E. / Bingman, C.A. / Kim, H.J. / Han, B.W. / Phillips, G.N.

History

Deposition	Apr 5, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 18, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Jun 8, 2016	Group: Database references
Revision 1.4	Oct 18, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2gm3.cif.gz	185.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2gm3.ent.gz	156.4 KB	Display	PDB format
PDBx/mmJSON format	2gm3.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/gm/2gm3 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/2gm3	HTTPS FTP

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Related structure data

Similar structure data	2n8r-d 5e5p-d 6yhu-d 1962 3eh8-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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.12922

Similar structure data

Other databases

TargetDB: GO.12922

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: unknown protein

B: unknown protein

C: unknown protein

D: unknown protein

E: unknown protein

F: unknown protein

hetero molecules

120 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: unknown protein

B: unknown protein

hetero molecules

defined by author&software
40.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: unknown protein

D: unknown protein

hetero molecules

defined by author&software
40.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: unknown protein

F: unknown protein

hetero molecules

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

4

C: unknown protein

E: unknown protein

hetero molecules

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

5

A: unknown protein

hetero molecules

D: unknown protein

hetero molecules

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

6

B: unknown protein

hetero molecules

F: unknown protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.351, 65.662, 73.014
Angle α, β, γ (deg.)	75.45, 75.04, 66.11
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 2

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	VAL	A	A	5 - 55	5 - 55
2	1	1	PRO	VAL	B	B	5 - 55	5 - 55
3	1	1	PRO	VAL	C	C	5 - 55	5 - 55
4	1	1	PRO	VAL	D	D	5 - 55	5 - 55
5	1	1	PRO	VAL	E	E	5 - 55	5 - 55
6	1	1	PRO	VAL	F	F	5 - 55	5 - 55
7	2	1	GLY	ASP	A	A	85 - 174	85 - 174
8	2	1	GLY	ASP	B	B	85 - 174	85 - 174
9	2	1	GLY	ASP	C	C	85 - 174	85 - 174
10	2	1	GLY	ASP	D	D	85 - 174	85 - 174
11	2	1	GLY	ASP	E	E	85 - 174	85 - 174
12	2	1	GLY	ASP	F	F	85 - 174	85 - 174
1	1	2	SER	MSE	A	A	66 - 77	66 - 77
2	1	2	SER	MSE	B	B	66 - 77	66 - 77
3	1	2	SER	MSE	C	C	66 - 77	66 - 77
4	1	2	SER	MSE	D	D	66 - 77	66 - 77
5	1	2	SER	MSE	D	D	66 - 77	66 - 77
6	1	2	SER	MSE	F	F	66 - 77	66 - 77

NCS ensembles :

ID
1
2

Details

The biological unit is a dimer. There are 3 biological units in the asymmetric unit (chains A & B and chains C & D and chains E & F).

#1: Protein	unknown protein Mass: 19691.934 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g01520 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834 P(RARE2) / References: UniProt: Q8LGG8
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate Mass: 347.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.24 Å³/Da / Density % sol: 45 %
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 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (18% PEG 2K, 5% DMSO, 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 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (18% PEG 2K, 5% DMSO, 0.10 M PIPES PH 6.5) Crystals cryo-protected with 20% PEG 2K, 0.1 M TRIS PH 8, and a final concentration of 20 % Ethylene glycol, temperature 293K, VAPOR DIFFUSION, HANGING DROP

Crystal

Density Matthews: 2.24 Å³/Da / Density % sol: 45 %

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 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (18% PEG 2K, 5% DMSO, 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: 0.97934 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 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: 0.97934 Å / Relative weight: 1

Reflection

Resolution: 2.5→40.7 Å / Num. obs: 36006 / % possible obs: 97.2 % / Redundancy: 3.7 % / R_merge(I) obs: 0.058 / Χ²: 1.305 / Net I/σ(I): 9.913

Reflection shell

Resolution: 2.5→2.59 Å / Redundancy: 3 % / R_merge(I) obs: 0.239 / Mean I/σ(I) obs: 4.406 / Num. unique all: 3309 / Χ²: 1.131 / % possible all: 89.4

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Phasing

Phasing dm

FOM : 0.66 / FOM acentric: 0.66 / FOM centric: 0 / Reflection: 36473 / Reflection acentric: 36473 / Reflection centric: 0

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	Reflection	Reflection acentric
7-69.559	0.94	0.94	1592	1592
4.4-7	0.89	0.89	4930	4930
3.5-4.4	0.85	0.85	6218	6218
3.1-3.5	0.69	0.69	6285	6285
2.6-3.1	0.52	0.52	11158	11158
2.5-2.6	0.44	0.44	6290	6290

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
RESOLVE	2.06	phasing
REFMAC	5.2.0005	refinement
PDB_EXTRACT	1.701	data extraction
SHELXE		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.461→40.7 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.914 / WR_factor R_free: 0.288 / WR_factor R_work: 0.24 / SU B: 18.763 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.651 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2607	1800	4.999 %	Random
R_work	0.2185	-	-	-
all	0.221	-	-	-
obs	0.22065	36006	96.822 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 60.244 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.171 Å²	-0.933 Å²	1.28 Å²
2-	-	0.245 Å²	-0.48 Å²
3-	-	-	0.262 Å²

Refinement step

Cycle: LAST / Resolution: 2.461→40.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7084	0	138	13	7235

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	7380
X-RAY DIFFRACTION	r_angle_refined_deg	1.501	1.977	9995
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.675	5	889
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.463	24.007	307
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.647	15	1286
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.711	15	47
X-RAY DIFFRACTION	r_chiral_restr	0.374	0.2	1146
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5395
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	3463
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	5031
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	257
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.196	0.2	111
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.262	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	0.573	1.5	4623
X-RAY DIFFRACTION	r_mcangle_it	0.942	2	7371
X-RAY DIFFRACTION	r_scbond_it	1.445	3	3097
X-RAY DIFFRACTION	r_scangle_it	2.18	4.5	2622

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	532	TIGHT POSITIONAL	0.07	0.05
1	2	B	532	TIGHT POSITIONAL	0.06	0.05
1	3	C	532	TIGHT POSITIONAL	0.05	0.05
1	4	D	532	TIGHT POSITIONAL	0.06	0.05
1	5	E	532	TIGHT POSITIONAL	0.04	0.05
1	6	F	532	TIGHT POSITIONAL	0.05	0.05
1	1	A	500	MEDIUM POSITIONAL	0.48	0.5
1	2	B	500	MEDIUM POSITIONAL	0.61	0.5
1	3	C	500	MEDIUM POSITIONAL	0.38	0.5
1	4	D	500	MEDIUM POSITIONAL	0.62	0.5
1	5	E	500	MEDIUM POSITIONAL	0.42	0.5
1	6	F	500	MEDIUM POSITIONAL	0.72	0.5
1	1	A	532	TIGHT THERMAL	0.12	0.5
1	2	B	532	TIGHT THERMAL	0.1	0.5
1	3	C	532	TIGHT THERMAL	0.11	0.5
1	4	D	532	TIGHT THERMAL	0.1	0.5
1	5	E	532	TIGHT THERMAL	0.1	0.5
1	6	F	532	TIGHT THERMAL	0.09	0.5
1	1	A	500	MEDIUM THERMAL	0.8	2
1	2	B	500	MEDIUM THERMAL	0.66	2
1	3	C	500	MEDIUM THERMAL	0.73	2
1	4	D	500	MEDIUM THERMAL	0.78	2
1	5	E	500	MEDIUM THERMAL	0.57	2
1	6	F	500	MEDIUM THERMAL	0.64	2
2	1	A	47	TIGHT POSITIONAL	0.05	0.05
2	2	B	47	TIGHT POSITIONAL	0.05	0.05
2	3	C	47	TIGHT POSITIONAL	0.04	0.05
2	4	D	47	TIGHT POSITIONAL	0.03	0.05
2	2	E	47	TIGHT POSITIONAL	0.03	0.05
2	6	F	47	TIGHT POSITIONAL	0.07	0.05
2	1	A	47	MEDIUM POSITIONAL	0.59	0.5
2	2	B	47	MEDIUM POSITIONAL	0.74	0.5
2	3	C	47	MEDIUM POSITIONAL	0.71	0.5
2	4	D	47	MEDIUM POSITIONAL	0.74	0.5
2	2	E	47	MEDIUM POSITIONAL	0.74	0.5
2	6	F	47	MEDIUM POSITIONAL	0.93	0.5
2	1	A	47	TIGHT THERMAL	0.24	0.5
2	2	B	47	TIGHT THERMAL	0.2	0.5
2	3	C	47	TIGHT THERMAL	0.08	0.5
2	4	D	47	TIGHT THERMAL	0.11	0.5
2	2	E	47	TIGHT THERMAL	0.11	0.5
2	6	F	47	TIGHT THERMAL	0.22	0.5
2	1	A	47	MEDIUM THERMAL	0.74	2
2	2	B	47	MEDIUM THERMAL	1.25	2
2	3	C	47	MEDIUM THERMAL	0.45	2
2	4	D	47	MEDIUM THERMAL	0.73	2
2	2	E	47	MEDIUM THERMAL	0.73	2
2	6	F	47	MEDIUM THERMAL	1	2

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	R_factor all	Num. reflection all	% reflection obs (%)
2.461-2.525	0.328	122	0.293	2234	0.295	2827	83.339
2.525-2.594	0.351	131	0.276	2330	0.28	2632	93.503
2.594-2.669	0.365	144	0.26	2353	0.266	2577	96.896
2.669-2.751	0.283	111	0.257	2398	0.258	2554	98.238
2.751-2.842	0.287	112	0.25	2304	0.252	2462	98.132
2.842-2.941	0.273	106	0.242	2231	0.243	2371	98.566
2.941-3.052	0.3	105	0.226	2148	0.229	2290	98.384
3.052-3.176	0.237	104	0.23	2081	0.23	2218	98.512
3.176-3.317	0.289	119	0.215	1949	0.219	2086	99.137
3.317-3.479	0.277	88	0.226	1918	0.228	2032	98.72
3.479-3.666	0.236	94	0.223	1800	0.224	1911	99.11
3.666-3.888	0.261	87	0.212	1697	0.214	1812	98.455
3.888-4.156	0.228	84	0.2	1607	0.201	1710	98.889
4.156-4.487	0.222	79	0.175	1476	0.177	1576	98.668
4.487-4.913	0.199	73	0.18	1363	0.181	1463	98.154
4.913-5.49	0.282	66	0.216	1248	0.219	1324	99.245
5.49-6.333	0.312	53	0.242	1103	0.244	1161	99.569
6.333-7.74	0.29	57	0.229	921	0.233	988	98.988
7.74-10.879	0.193	43	0.174	702	0.175	769	96.879
10.879-69.505	0.352	22	0.288	343	0.291	425	85.882

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	5.4108	1.4193	-0.1523	4.4523	-0.2475	4.1196	0.0453	0.2363	-0.0413	0.144	-0.2015	-0.1017	-0.2305	0.056	0.1563	-0.2876	-0.025	-0.0661	-0.3186	-0.0079	-0.288	26.288	18.69	61.014
2	5.0451	0.1191	-0.8468	6.966	-0.4097	4.8572	0.0519	-0.44	-0.6623	0.7369	-0.1345	0.4562	0.4284	-0.5162	0.0827	-0.1569	-0.1989	0.1031	-0.0546	-0.05	-0.1121	10.543	4.434	72.917
3	6.7747	0.5106	-0.0132	3.9315	-0.2841	4.6136	0.327	0.1891	0.1657	-0.0663	-0.282	-0.6015	-0.303	0.3792	-0.0449	-0.2626	0.0342	0.0601	-0.3014	0.0638	-0.2095	-5.702	-13.027	39.772
4	6.7994	1.1305	-1.3701	4.1935	0.0124	4.9359	0.3092	-0.3275	-0.1521	0.1691	-0.2282	0.3321	-0.0468	-0.462	-0.0811	-0.3098	0.0132	-0.0048	-0.2228	0.0176	-0.2983	-28.589	-18.57	47.871
5	6.4943	1.6583	-0.1615	7.5561	-0.0716	4.9389	-0.0934	0.1138	-0.2222	0.6677	0.5443	0.2876	0.4132	-0.3493	-0.451	-0.0845	0.0662	-0.0081	-0.1479	0.0604	-0.2691	27.976	9.57	23.521
6	3.2234	-0.1391	-0.3732	10.2477	-0.8683	4.8517	0.0976	0.0097	0.6178	0.2502	0.5819	-1.917	-0.5155	0.517	-0.6795	-0.1747	-0.015	0.0693	-0.0512	-0.2995	0.325	45.482	27.346	20.954

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	5 - 55	5 - 55
2	1	A	A	80 - 174	80 - 174
3	2	B	B	5 - 55	5 - 55
4	2	B	B	85 - 174	85 - 174
5	3	C	C	5 - 55	5 - 55
6	3	C	C	80 - 174	80 - 174
7	4	D	D	5 - 55	5 - 55
8	4	D	D	80 - 174	80 - 174
9	5	E	E	5 - 55	5 - 55
10	5	E	E	80 - 174	80 - 174
11	6	F	F	5 - 55	5 - 55
12	6	F	F	79 - 174	79 - 174

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Experimental details

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