PDB-4obt: Crystal structure of Arabidopsis thaliana cytosolic triose phosph...

ID or keywords:

Entry

Database: PDB / ID: 4obt

Title

Crystal structure of Arabidopsis thaliana cytosolic triose phosphate isomerase

Components

Triosephosphate isomerase, cytosolic

Keywords

ISOMERASE / TIM Barrel / Glycolysis / Citosolyc

Function / homology

Function and homology information

plant-type cell wall / apoplast / plasmodesma / plant-type vacuole / triose-phosphate isomerase / triose-phosphate isomerase activity / chloroplast stroma / response to zinc ion / chloroplast / gluconeogenesis ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Lopez-Castillo, M. / Jimenez-Sandoval, P. / Lara-Gonzalez, S. / Brieba, L.G. / Baruch, N.

Citation

Journal: Front Plant Sci / Year: 2016
Title: Structural Basis for Redox Regulation of Cytoplasmic and Chloroplastic Triosephosphate Isomerases from Arabidopsis thaliana.
Authors: Lopez-Castillo, L.M. / Jimenez-Sandoval, P. / Baruch-Torres, N. / Trasvina-Arenas, C.H. / Diaz-Quezada, C. / Lara-Gonzalez, S. / Winkler, R. / Brieba, L.G.

History

Deposition	Jan 7, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 25, 2017	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4obt.cif.gz	200.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4obt_validation.pdf.gz	417.3 KB	Display	wwPDB validaton report
Full document	4obt_full_validation.pdf.gz	418.9 KB	Display
Data in XML	4obt_validation.xml.gz	22 KB	Display
Data in CIF	4obt_validation.cif.gz	32.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ob/4obt ftp://data.pdbj.org/pub/pdb/validation_reports/ob/4obt	HTTPS FTP

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Related structure data

Related structure data	4ohqC C: citing same article (ref.)
Similar structure data	5bmw-d 4ywi-d 1r2r-1 1lzo-2 6nxq-1 5bmx-1 1vga-2 1m7p-d 1woa-1 3psv-d 4nvt-2 5bnk-d 6nlh-3 3ta6-d 2vfe-d 1lzo-1 6nxr-1 2vfg-2 1wob-1 6cg9-d Search similar-shape structures by Omokage search (details) 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	#50 - Feb 2004 Glycolytic Enzymes similarity (8)

Deposited unit

A: Triosephosphate isomerase, cytosolic

B: Triosephosphate isomerase, cytosolic

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	77.940, 84.590, 89.720
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Triosephosphate isomerase, cytosolic / TIM / Triose-phosphate isomerase Mass: 27489.318 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Columbia / Gene: At3g55440, CTIMC, T22E16.100, TPI / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P48491, triose-phosphate isomerase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Triosephosphate isomerase, cytosolic / TIM / Triose-phosphate isomerase

Mass: 27489.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Strain: Columbia / Gene: At3g55440, CTIMC, T22E16.100, TPI / Plasmid: pET28 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P48491, triose-phosphate isomerase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.67 Å³/Da / Density % sol: 53.95 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.09 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.09 Å / Relative weight: 1
Reflection	Resolution: 1.6→38.97 Å / Num. all: 78790 / Num. obs: 78784 / % possible obs: 99.9 % / Observed criterion σ(F): -96.453 / Observed criterion σ(I): 15.478

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→38.97 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 17.49 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1889	2000	2.54 %
R_work	0.1662	-	-
obs	0.1668	78784	99.96 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 23.4893 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→38.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3655	0	0	372	4027

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3792
X-RAY DIFFRACTION	f_angle_d	1.141	5187
X-RAY DIFFRACTION	f_dihedral_angle_d	11.237	1303
X-RAY DIFFRACTION	f_chiral_restr	0.05	606
X-RAY DIFFRACTION	f_plane_restr	0.007	681

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.6-1.64	0.2395	132	0.2047	5420	X-RAY DIFFRACTION	100
1.64-1.6844	0.2039	145	0.1868	5403	X-RAY DIFFRACTION	100
1.6844-1.7339	0.2119	146	0.188	5428	X-RAY DIFFRACTION	100
1.7339-1.7899	0.2017	123	0.1741	5457	X-RAY DIFFRACTION	100
1.7899-1.8539	0.1716	154	0.1607	5428	X-RAY DIFFRACTION	100
1.8539-1.9281	0.2033	144	0.1666	5421	X-RAY DIFFRACTION	100
1.9281-2.0158	0.2038	134	0.1663	5473	X-RAY DIFFRACTION	100
2.0158-2.1221	0.1879	147	0.167	5438	X-RAY DIFFRACTION	100
2.1221-2.255	0.1917	149	0.1651	5469	X-RAY DIFFRACTION	100
2.255-2.4291	0.1797	141	0.1671	5504	X-RAY DIFFRACTION	100
2.4291-2.6735	0.2128	145	0.1752	5467	X-RAY DIFFRACTION	100
2.6735-3.0603	0.1992	138	0.1761	5526	X-RAY DIFFRACTION	100
3.0603-3.8551	0.1876	149	0.1641	5598	X-RAY DIFFRACTION	100
3.8551-38.9815	0.1615	153	0.1486	5752	X-RAY DIFFRACTION	99

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	0.6293	-0.0291	-0.0969	0.7605	-0.1328	0.8488	0.0139	-0.0642	0.0208	-0.0409	-0.0366	-0.0417	0.0397	0.1368	0.0262	0.1175	-0.0079	-0.018	0.1527	0.0267	0.1608	-6.5799	-13.1352	5.9818
2	0.3533	-0.0407	-0.1737	0.3864	-0.6057	3.7047	-0.0086	0.033	0.1079	-0.0062	-0.0292	-0.0753	-0.2246	0.1479	0.0212	0.1969	-0.0477	-0.0518	0.1989	0.0336	0.2106	-4.2858	-0.3392	14.4053
3	0.3708	-0.0002	-0.2113	0.4412	0.0459	0.742	0.0151	0.0155	0.0628	0.0718	-0.048	0.0456	-0.1118	-0.0282	0.0349	0.1097	-0.0073	-0.013	0.1449	0.022	0.1469	-14.9733	-10.8338	11.0168
4	0.7284	0.0811	-0.1641	0.6801	-0.0069	1.1799	-0.0822	0.0005	-0.1031	0.0512	-0.0585	-0.0787	0.1873	0.0148	0.0964	0.0931	0.0134	0.0161	0.1218	0.0078	0.1411	-13.6866	-25.4537	7.9243
5	0.9274	0.1208	-0.3111	1.0495	0.1157	0.3073	-0.052	-0.1577	-0.0728	-0.0954	-0.0323	-0.0497	0.1548	0.092	0.0699	0.1195	0.038	0.0264	0.2331	0.0189	0.1645	-5.0697	-25.1676	2.2243
6	2.9047	0.9234	0.5882	1.8089	0.2881	1.85	0.1291	0.2035	-0.2015	-0.2696	-0.069	-0.0433	0.3242	0.1126	-0.012	0.153	0.0101	0.0143	0.1754	-0.0117	0.1565	-7.666	-28.1948	-8.3164
7	0.2406	0.0119	-0.1189	0.7793	0.1884	0.7232	-0.0632	0.048	-0.0169	-0.0864	0.0115	-0.251	-0.0458	0.3082	0.0543	0.1117	-0.0059	-0.0029	0.2221	0.0319	0.188	-1.3925	-16.2931	0.1899
8	2.0269	0.3631	-0.2411	2.9616	0.8336	1.8744	-0.0967	0.2571	0.0885	-0.1986	0.0066	-0.3313	-0.1015	0.2298	0.0111	0.128	-0.0206	-0.0047	0.2697	0.0726	0.2583	0.878	-7.192	0.3002
9	0.7322	-0.033	-0.2102	0.1436	-0.1549	0.7124	-0.0412	0.011	-0.0316	0.3808	-0.0671	0.1838	0.0801	-0.0415	-0.0073	0.35	-0.0122	0.0682	0.1485	-0.0145	0.1607	-27.1022	-16.6749	36.543
10	0.3231	-0.0567	-0.8107	0.5217	1.0524	4.7958	0.1176	-0.0724	0.0259	0.0131	-0.2373	0.1768	-0.0596	-0.2021	0.0651	0.1692	-0.0132	0.0288	0.2128	-0.0623	0.2314	-33.4208	-5.5797	27.9644
11	0.5238	-0.1499	-0.355	0.4682	0.1932	0.4968	0.0612	-0.0293	0.1376	0.2408	-0.0843	0.0407	-0.0058	-0.0442	0.0308	0.2001	-0.0192	0.0383	0.153	-0.0148	0.1543	-24.4498	-8.4236	34.1112
12	0.5919	-0.0446	-0.1956	0.782	0.1472	0.9353	-0.0583	-0.0484	-0.0355	0.3264	-0.0058	-0.0615	0.2387	0.188	0.0584	0.2205	0.0222	-0.0193	0.1668	0.0235	0.1342	-12.3926	-20.9714	29.4426
13	0.2687	-0.3121	-0.1616	0.4151	0.0775	0.241	-0.1188	-0.214	-0.2468	0.8092	-0.048	0.1169	0.5582	0.1485	-0.1062	0.7301	-0.0259	0.0682	0.1565	0.0332	0.2423	-19.5615	-30.1769	39.8101
14	0.2393	0.1568	-0.0128	0.1797	-0.068	0.1398	-0.0301	0.1072	0.0254	0.1069	-0.004	0.0956	0.0628	-0.0423	-0.1905	0.8752	-0.2333	0.4322	0.1406	0.1375	0.221	-32.9181	-32.4285	42.5534
15	0.0245	-0.1128	-0.0083	0.8539	-0.5193	1.0012	-0.1627	-0.14	-0.1113	0.927	-0.1892	0.517	0.5258	-0.1617	-0.6701	0.7742	-0.0316	0.1622	0.2474	-0.0107	0.1221	-27.682	-23.5755	44.5176
16	1.0632	-0.3096	-0.5115	1.8471	0.3529	1.7906	-0.0366	-0.158	-0.0366	0.2998	-0.1202	0.2468	0.1632	-0.1602	0.036	0.3187	-0.1343	0.2012	0.2116	-0.1877	0.3029	-36.3902	-13.4378	41.8552

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:15)
2	X-RAY DIFFRACTION	2	(chain A and resid 16:31)
3	X-RAY DIFFRACTION	3	(chain A and resid 32:79)
4	X-RAY DIFFRACTION	4	(chain A and resid 80:153)
5	X-RAY DIFFRACTION	5	(chain A and resid 154:181)
6	X-RAY DIFFRACTION	6	(chain A and resid 182:200)
7	X-RAY DIFFRACTION	7	(chain A and resid 201:239)
8	X-RAY DIFFRACTION	8	(chain A and resid 240:252)
9	X-RAY DIFFRACTION	9	(chain B and resid 1:15)
10	X-RAY DIFFRACTION	10	(chain B and resid 16:31)
11	X-RAY DIFFRACTION	11	(chain B and resid 32:65)
12	X-RAY DIFFRACTION	12	(chain B and resid 66:119)
13	X-RAY DIFFRACTION	13	(chain B and resid 120:169)
14	X-RAY DIFFRACTION	14	(chain B and resid 170:188)
15	X-RAY DIFFRACTION	15	(chain B and resid 189:239)
16	X-RAY DIFFRACTION	16	(chain B and resid 240:252)

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