PDB-2x0n: Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase ...

ID or keywords:

Entry

Database: PDB / ID: 2x0n

Title

Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma brucei determined from Laue data

Components

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

Keywords

OXIDOREDUCTASE / GLYCOLYSIS / GLYCOSOME

Function / homology

Function and homology information

glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glycosome / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol
Similarity search - Function

Biological species

TRYPANOSOMA BRUCEI BRUCEI (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Vellieux, F.M.D. / Hajdu, J. / Hol, W.G.J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma Brucei Determined from Laue Data.
Authors: Vellieux, F.M.D. / Hajdu, J. / Verlinde, C.L. / Groendijk, H. / Read, R.J. / Greenhough, T.J. / Campbell, J.W. / Kalk, K.H. / Littlechild, J.A. / Watson, H.C.

History

Deposition	Dec 16, 2009	Deposition site: PDBE / Processing site: PDBE
Supersession	Dec 22, 2009	ID: 1GGA
Revision 1.0	Dec 22, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jan 25, 2017	Group: Data collection
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2x0n.cif.gz	807.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2x0n.ent.gz	676.3 KB	Display	PDB format
PDBx/mmJSON format	2x0n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2x0n_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	2x0n_full_validation.pdf.gz	2 MB	Display
Data in XML	2x0n_validation.xml.gz	83.3 KB	Display
Data in CIF	2x0n_validation.cif.gz	107.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/2x0n ftp://data.pdbj.org/pub/pdb/validation_reports/x0/2x0n	HTTPS FTP

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Related structure data

Related structure data	1gd1S S: Starting model for refinement
Similar structure data	1ml3-d 1k3t-d 1gyp-d 1i32-2 1i33-2 1gyq-d 3dmt-d 1qxs-d 1i33-1 3ids-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (10)

Deposited unit

A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

B: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

O: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

P: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

Q: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

R: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

hetero molecules

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

1

A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

B: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

hetero molecules

A: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

B: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

hetero molecules

defined by author&software
160 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

O: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

P: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

Q: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

R: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL

hetero molecules

defined by author&software
160 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	135.520, 256.270, 114.910
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, GLYCOSOMAL / GADPH Mass: 39091.656 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) References: UniProt: P22512, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal	Density Matthews: 4.27 Å³/Da / Density % sol: 71.17 % / Description: NONE
Crystal grow	pH: 6.5 Details: PROTEIN: 5 MICROL OF 6 MG/ML GGAPDH IN 25 MM TRIS HCL PH 7.8, 0.6M AMMONIUM SULPHATE, 2MM NAD, 1MM DITHIOTHREITOL 1MM NA AZIDE, 1 MM EDTA. PRECIPITANT: 5 MICROL OF 52% SATURATED AMMONIUM ...Details: PROTEIN: 5 MICROL OF 6 MG/ML GGAPDH IN 25 MM TRIS HCL PH 7.8, 0.6M AMMONIUM SULPHATE, 2MM NAD, 1MM DITHIOTHREITOL 1MM NA AZIDE, 1 MM EDTA. PRECIPITANT: 5 MICROL OF 52% SATURATED AMMONIUM SULPHATE, 0.2M N,N-BIS-(2-HYDROXYETHYL)-2-AMINOETHANE SULFONIC ACID PH 6.5, 1MM DITHIOTHREITOL, 1MM NA AZIDE, 1MM EDTA, 20MM 3-PHOSPHOGLYCERATE. RESERVOIR: 1 ML

Crystal

Density Matthews: 4.27 Å³/Da / Density % sol: 71.17 % / Description: NONE

Crystal grow

pH: 6.5
Details: PROTEIN: 5 MICROL OF 6 MG/ML GGAPDH IN 25 MM TRIS HCL PH 7.8, 0.6M AMMONIUM SULPHATE, 2MM NAD, 1MM DITHIOTHREITOL 1MM NA AZIDE, 1 MM EDTA. PRECIPITANT: 5 MICROL OF 52% SATURATED AMMONIUM ...

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Data collection

Diffraction

Mean temperature: 273 K

Diffraction source

Source:

SYNCHROTRON / Site:

SRS

/ Beamline: PX9.7 / Wavelength: 0.489-1.905

Detector

Type: CEA / Detector: FILM

Radiation

Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.489	1
2	1.905	1

Reflection

Resolution: 3.2→7.4 Å / Num. obs: 34991 / % possible obs: 57 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / B_iso Wilson estimate: 34.93 Å² / R_merge(I) obs: 0.15 / Net I/σ(I): 7.2

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
DARESBURY	LAUE PROCESSING SOFTWARE	data reduction
DARESBURY	LAUE PROCESSING SOFTWARE	data scaling
MERLOT		phasing
BIOMOL		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GD1

1gd1

Resolution: 3.2→7.399 Å / SU ML: 0.34 / σ(F): 2.37 / Phase error: 18.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2182	1798	5.1 %
R_work	0.1498	-	-
obs	0.1533	34991	57.28 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 60.002 Å² / k_sol: 0.318 e/Å³

Displacement parameters

B_iso mean: 34.75 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.9115 Å²	-0 Å²	-0 Å²
2-	-	-0.717 Å²	0 Å²
3-	-	-	-2.7097 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→7.399 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16410	0	324	0	16734

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	17046
X-RAY DIFFRACTION	f_angle_d	1.492	23142
X-RAY DIFFRACTION	f_dihedral_angle_d	22.284	6348
X-RAY DIFFRACTION	f_chiral_restr	0.12	2670
X-RAY DIFFRACTION	f_plane_restr	0.005	2910

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 (%)
3.2-3.3045	0.344	127	0.2803	2227	X-RAY DIFFRACTION	39
3.3045-3.4242	0.2923	145	0.2404	2599	X-RAY DIFFRACTION	45
3.4242-3.5633	0.2788	174	0.2061	2958	X-RAY DIFFRACTION	52
3.5633-3.7282	0.2609	155	0.1738	3327	X-RAY DIFFRACTION	58
3.7282-3.9286	0.2197	189	0.1494	3691	X-RAY DIFFRACTION	64
3.9286-4.1804	0.1925	204	0.1231	3913	X-RAY DIFFRACTION	68
4.1804-4.5125	0.1746	246	0.1055	4080	X-RAY DIFFRACTION	71
4.5125-4.9838	0.1725	233	0.103	4112	X-RAY DIFFRACTION	71
4.9838-5.7452	0.1721	202	0.1167	3917	X-RAY DIFFRACTION	67
5.7452-7.3992	0.222	123	0.1575	2369	X-RAY DIFFRACTION	40

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	0.0611	0.0874	-0.0794	0.1828	-0.1552	0.1344	-0.0265	-0.0973	-0.0348	-0.0959	-0.0973	-0.174	0.1043	0.0693	0.1344	-0.023	-0.0065	0.1839	0.1143	0.2146	0.0144	89.1885	8.0489	34.5508
2	0.0442	-0.124	0.0172	0.1889	-0.0645	0.0367	0.0405	0.0509	0.058	-0.1437	-0.1109	-0.0082	-0.0471	0.0114	0.0199	-0.1647	0.2354	-0.014	-0.1746	0.0742	-0.0147	69.242	23.3866	44.4335
3	0.0111	0.0076	0.0157	0.0045	0.0102	0.0217	0.0058	0.0063	0.0038	-0.0079	-0.0132	-0.0017	-0.0027	0.0179	0.0058	0.2673	0.0105	0.1417	0.1633	0.0256	0.2273	83.0746	28.3115	22.1668
4	0.1447	0.3691	-0.1172	1.0026	-0.231	0.1452	0.0605	0.0165	0.0939	0.0973	-0.0727	0.3763	0.0431	-0.0535	-0.0064	-0.0632	-0.156	0.1407	0.0174	-0.0385	0.0775	42.9624	-1.6829	77.0839
5	0.0987	-0.1507	-0.1351	0.3021	0.2497	0.2591	0.0286	0.0411	-0.0289	0.1461	-0.2582	0.1778	-0.0092	-0.2198	0.118	-0.1946	0.0866	0.0036	0.0265	-0.0377	0.0286	56.28	18.9409	66.5584
6	0.0279	-0.0057	0.0163	0.005	-0.0006	0.0115	-0.0095	0.0046	-0.0106	0.0011	0.0019	-0.0002	0.0105	-0.0051	0.0087	0.3765	-0.0716	0.105	0.3173	-0.0569	0.3666	38.2156	12.8661	90.2994
7	0.1878	-0.1452	0.1012	0.1932	0.0129	0.1763	-0.044	0.2697	0.1885	0.0395	-0.0321	-0.1544	0.0187	0.1474	0.1089	0.0358	-0.0646	-0.0679	0.2012	0.1915	0.1963	29.8915	87.3173	-0.8381
8	0.362	-0.0873	0.2322	0.2465	-0.0246	0.4003	-0.1096	0.0437	0.0975	0.0124	-0.0337	-0.0194	-0.0078	-0.0929	0.1276	0.0655	-0.0169	-0.0317	0.0718	-0.0035	0.0648	6.264	80.5067	9.4554
9	0.0182	-0.0073	0.0128	0.0153	0.0025	0.0136	-0.0055	-0.0098	-0.0094	-0.0141	-0.0036	-0.0046	-0.0224	0.0278	0.0101	0.168	0.0356	0.048	0.1828	0.0682	0.1817	17.5322	96.499	-14.0008
10	0.3502	-0.0481	-0.0532	0.0032	0.019	0.4084	-0.097	0.0077	-0.2632	0.1092	-0.0265	0.1231	0.3377	0.0288	0.1715	0.2234	0.0181	0.1944	-0.0439	0.0111	0.2326	1.2976	47.8161	39.9135
11	0.1916	-0.2508	-0.0986	0.7907	0.1934	0.547	-0.074	0.0355	-0.0643	0.2403	-0.0193	0.0473	-0.0296	-0.0962	0.1193	0.066	0.0012	0.0118	-0.0022	-0.0147	0.0333	0.4982	72.4538	29.6913
12	0.0129	0.0115	-0.0113	0.0099	-0.0097	0.01	-0.0071	0.0074	0.0085	0.0033	-0.0143	-0.0093	0.0141	0.0092	0.0212	0.3314	-0.057	0.1551	0.2254	0.0074	0.3456	-11.226	56.8256	53.0159
13	0.4179	-0.0527	-0.1422	0.1658	0.0653	0.1281	0.0399	0.1804	-0.3147	0.0088	-0.1382	0.1954	0.0032	-0.0706	0.1193	0.0446	-0.0077	0.0317	0.2236	-0.2354	0.2634	7.7225	45.2616	-2.675
14	1.0509	-0.2371	-0.342	0.1773	0.1216	0.4848	-0.0993	0.1872	-0.1309	0.0738	-0.0696	0.0689	-0.0577	0.0743	0.119	0.073	0.0122	0.077	0.0941	-0.0347	0.0334	32.8251	43.6756	7.3838
15	0.0293	0.0342	0.0016	0.0435	0.008	0.0112	-0.0172	0.0061	0.0198	-0.0047	-0.0193	0.0114	0.0015	-0.0034	0.0332	0.1821	-0.0599	0.029	0.3358	-0.1196	0.3822	24.475	32.1481	-15.0799
16	0.1423	-0.1042	0.0795	0.0738	-0.0475	0.0505	-0.1247	-0.0219	0.2444	0.0858	0.0504	-0.0959	-0.0736	0.0123	0.0998	0.0909	0.0358	-0.1529	0.0003	-0.0496	0.2689	40.1588	78.9265	40.5324
17	0.2094	-0.1685	0.0998	0.3403	-0.049	0.1149	-0.1511	-0.099	0.0427	0.1142	0.1043	0.004	0.0136	0.0288	0.01	0.0363	0.0453	-0.0438	0.0152	0.0395	-0.0231	41.0709	54.5557	29.6417
18	-0.0001	0.0001	-0.0001	-0	-0	0.0001	0.0161	0.0009	-0.0016	-0.0002	0.0143	-0.0062	-0.0042	0.0051	-0.0291	0.1846	0.0055	0.0551	0.2082	0.0416	0.3417	52.4425	69.7229	53.7338

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 1:114)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 115:351)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 352:358)
4	X-RAY DIFFRACTION	4	(CHAIN B AND RESID 1:163)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 164:351)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 352:358)
7	X-RAY DIFFRACTION	7	(CHAIN O AND RESID 1:164)
8	X-RAY DIFFRACTION	8	(CHAIN O AND RESID 165:351)
9	X-RAY DIFFRACTION	9	(CHAIN O AND RESID 352:358)
10	X-RAY DIFFRACTION	10	(CHAIN P AND RESID 1:164)
11	X-RAY DIFFRACTION	11	(CHAIN P AND RESID 165:351)
12	X-RAY DIFFRACTION	12	(CHAIN P AND RESID 352:358)
13	X-RAY DIFFRACTION	13	(CHAIN Q AND RESID 1:113)
14	X-RAY DIFFRACTION	14	(CHAIN Q AND RESID 114:351)
15	X-RAY DIFFRACTION	15	(CHAIN Q AND RESID 352:358)
16	X-RAY DIFFRACTION	16	(CHAIN R AND RESID 1:163)
17	X-RAY DIFFRACTION	17	(CHAIN R AND RESID 164:351)
18	X-RAY DIFFRACTION	18	(CHAIN R AND RESID 352:358)

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