PDB-4p8r: Structure of a glycosomal glyceraldehyde 3-phosphate dehydrogenas...

ID or keywords:

Entry

Database: PDB / ID: 4p8r

Title

Structure of a glycosomal glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma brucei

Components

Glyceraldehyde 3-phosphate dehydrogenase, cytosolic

Keywords

OXIDOREDUCTASE / SSGCID / glyceraldehyde 3-phosphate dehydrogenase / glycosomal / African trypanosomiasis Trypanosoma brucei / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

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

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Structure of a glycosomal glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma brucei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Lorimer, D. / Edwards, T.E.

History

Deposition	Mar 31, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 18, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 30, 2015	Group: Data collection
Revision 1.2	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4p8r.cif.gz	519.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4p8r.ent.gz	428.8 KB	Display	PDB format
PDBx/mmJSON format	4p8r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4p8r_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	4p8r_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4p8r_validation.xml.gz	54.8 KB	Display
Data in CIF	4p8r_validation.cif.gz	76.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p8/4p8r ftp://data.pdbj.org/pub/pdb/validation_reports/p8/4p8r	HTTPS FTP

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Related structure data

Similar structure data	4lsm-2 1s7c-1 6ok4-d 6nlx-d 1dc6-2 3rvd-3 2vyn-d 1hdg-1 3cif-d 6wyc-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
Other databases	TargetTrack: SSGCID-TrbrA.00855.a

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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, cytosolic

B: Glyceraldehyde 3-phosphate dehydrogenase, cytosolic

C: Glyceraldehyde 3-phosphate dehydrogenase, cytosolic

D: Glyceraldehyde 3-phosphate dehydrogenase, cytosolic

hetero molecules

149 kDa, 4 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)	86.700, 86.700, 701.370
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	Glyceraldehyde 3-phosphate dehydrogenase, cytosolic Mass: 36684.809 Da / Num. of mol.: 4 / Fragment: TrbrA.00855.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb10.6k15.3850 / Plasmid: TrbrA.00855.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q38AR9, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 691 / 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: 2.6 Å³/Da / Density % sol: 53 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Microlytics MGSC1 screen, e3: 30% PEG 550 MME, 20mM magnesium chloride, 100mM HEPEES/NaOH pH 7.5, TrbrA.00885.a.B1.PS01548 at 19.4 mg/ml, tray 236008e3, puck gzn0-7; cryo: direct

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 20, 2012

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.2→50 Å / Num. all: 1096712 / Num. obs: 81199 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.5 % / B_iso Wilson estimate: 25.99 Å² / R_merge F obs: 0.998 / R_merge(I) obs: 0.091 / R_rim(I) all: 0.095 / R_sym value: 0.091 / Χ²: 1.005 / Net I/av σ(I): 21.8 / Net I/σ(I): 21.81 / Num. measured all: 1096712

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.2-2.26		3.6	0.702	0.532	2.1	19513	5888	5494	0.626	93.3
2.26-2.32			0.806	0.465	2.78	25164	5754	5648	0.527	98.2
2.32-2.39			0.883	0.394	3.88	31629	5610	5595	0.434	99.7
2.39-2.46			0.922	0.36	4.86	38717	5457	5457	0.389	100
2.46-2.54			0.958	0.314	6.45	47032	5303	5303	0.333	100
2.54-2.63			0.977	0.272	8.62	56643	5141	5141	0.285	100
2.63-2.73			0.984	0.249	10.89	69276	4951	4951	0.259	100
2.73-2.84			0.992	0.202	15.46	89546	4764	4764	0.208	100
2.84-2.97			0.995	0.162	19.34	88752	4602	4602	0.166	100
2.97-3.11			0.997	0.127	24.78	85126	4435	4435	0.13	100
3.11-3.28			0.998	0.101	30.41	80415	4207	4207	0.104	100
3.28-3.48			0.999	0.083	36.34	76022	4035	4035	0.085	100
3.48-3.72			0.999	0.072	41.19	70230	3767	3767	0.074	100
3.72-4.02			0.999	0.064	45.38	65542	3555	3555	0.066	100
4.02-4.4			0.999	0.057	49.22	60550	3300	3300	0.058	100
4.4-4.92			0.999	0.052	51.53	54591	3003	3003	0.054	100
4.92-5.68			0.999	0.055	47.6	49231	2705	2705	0.056	100
5.68-6.96			0.999	0.057	43.21	41553	2336	2336	0.059	100
6.96-9.84			1	0.041	51.17	32100	1894	1894	0.042	100
	9.84		1	0.034	55.38	15080	1217	1007	0.035	82.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE	2.5.5	data scaling
PHASER		phasing
PDB_EXTRACT	3.14	data extraction
ARP		model building
PHENIX	(phenix.refine: dev_1659)	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→19.893 Å / FOM work R set: 0.8915 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1973	4164	5.14 %	Radom selection
R_work	0.1499	76796	-	-
obs	0.1524	80960	99.36 %	-

Solvent computation

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

Displacement parameters

B_iso max: 106.2 Å² / B_iso mean: 30.82 Å² / B_iso min: 11.04 Å²

Refinement step

Cycle: final / Resolution: 2.2→19.893 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9850	0	179	691	10720
B_iso mean	-	-	39.86	34.53	-
Num. residues	-	-	-	-	1323

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	10243
X-RAY DIFFRACTION	f_angle_d	1.072	13962
X-RAY DIFFRACTION	f_chiral_restr	0.043	1661
X-RAY DIFFRACTION	f_plane_restr	0.005	1788
X-RAY DIFFRACTION	f_dihedral_angle_d	13.519	3638

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.2-2.225	0.2829	130	0.2287	2313	2443	91
2.225-2.2511	0.2675	131	0.2165	2344	2475	95
2.2511-2.2785	0.276	134	0.2156	2515	2649	97
2.2785-2.3073	0.2579	146	0.1985	2398	2544	98
2.3073-2.3376	0.2654	141	0.1903	2518	2659	99
2.3376-2.3696	0.2286	124	0.1799	2484	2608	100
2.3696-2.4034	0.2473	135	0.1745	2560	2695	100
2.4034-2.4392	0.246	129	0.1741	2523	2652	100
2.4392-2.4773	0.2246	139	0.1722	2530	2669	100
2.4773-2.5178	0.2338	137	0.1631	2512	2649	100
2.5178-2.5611	0.2123	141	0.1577	2545	2686	100
2.5611-2.6076	0.1951	115	0.1487	2543	2658	100
2.6076-2.6576	0.234	153	0.1566	2484	2637	100
2.6576-2.7118	0.2332	133	0.1561	2604	2737	100
2.7118-2.7706	0.2	154	0.1552	2482	2636	100
2.7706-2.8349	0.2053	143	0.1517	2551	2694	100
2.8349-2.9055	0.2187	146	0.1666	2573	2719	100
2.9055-2.9838	0.2094	135	0.1637	2551	2686	100
2.9838-3.0713	0.2632	145	0.1642	2535	2680	100
3.0713-3.1701	0.2094	141	0.1587	2543	2684	100
3.1701-3.2829	0.2119	129	0.1691	2611	2740	100
3.2829-3.4137	0.2116	132	0.1604	2592	2724	100
3.4137-3.5682	0.2102	175	0.1519	2554	2729	100
3.5682-3.7552	0.2191	143	0.1489	2622	2765	100
3.7552-3.9887	0.1591	117	0.1361	2612	2729	100
3.9887-4.2938	0.1486	144	0.1126	2640	2784	100
4.2938-4.7207	0.1331	126	0.1048	2662	2788	100
4.7207-5.3918	0.1417	137	0.108	2724	2861	100
5.3918-6.7488	0.1448	145	0.1332	2738	2883	100
6.7488-19.8938	0.1511	164	0.1346	2933	3097	100

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	1.2738	-0.2114	-0.2674	0.897	-0.1027	1.0598	0.0062	-0.1982	0.1544	0.4359	-0.0341	-0.0906	-0.0671	0.1738	-0.0002	0.2823	-0.0458	-0.0478	0.2822	0.0322	0.1811	71.8218	-18.4506	57.8663
2	0.4739	-0.2001	-0.113	0.7876	-0.129	0.2185	-0.0649	-0.1848	-0.0279	0.1454	0.0265	-0.1687	-0.0476	0.1886	0.0451	0.1392	-0.0103	-0.0329	0.3394	0.0073	0.1929	80.3466	-10.7005	37.3843
3	0.564	0.1245	-0.1844	0.7425	-0.1071	0.8595	0.023	-0.1157	-0.1514	0.1033	-0.0724	-0.3011	0.1728	0.3551	0.0373	0.1429	0.0389	-0.0336	0.3524	0.0485	0.2343	85.4869	-27.0622	40.1356
4	1.6937	-0.0139	-0.0592	1.5622	0.2247	0.6406	0.0633	-0.3131	0.2286	0.048	-0.0016	0.1679	-0.2175	-0.0525	-0.0686	0.2043	0.01	0.0252	0.2774	-0.0212	0.2089	59.6387	13.9695	32.369
5	0.5171	0.0144	-0.1988	0.9562	-0.0435	0.2264	0.0116	0.0649	0.0523	-0.0751	0.0189	0.3775	-0.0761	-0.1722	-0.0002	0.1243	0.0206	-0.0304	0.3096	0.0254	0.3028	44.9473	-4.5395	24.5692
6	0.936	-0.2323	-0.4604	1.0793	-0.0663	1.3696	-0.0885	0.1697	0.0359	-0.4119	0.0831	0.1168	0.0308	-0.1227	-0.0346	0.2389	-0.0501	-0.0145	0.284	0.0356	0.1293	68.7682	-12.552	0.5874
7	0.9446	-0.3905	-0.2544	1.6036	0.5729	1.9608	-0.0181	0.1216	-0.1379	-0.5738	-0.0545	0.2376	-0.09	-0.2082	0.0109	0.3092	-0.0647	-0.05	0.2737	0.0358	0.1971	64.0303	-13.7933	-1.5011
8	0.9247	0.1347	0.0579	0.7562	-0.0818	1.0578	0.0113	0.0094	-0.1513	-0.2849	0.0133	-0.202	0.0614	0.2096	0.0031	0.2256	-0.0051	0.0821	0.2712	0.0029	0.2072	86.1467	-19.1295	4.8768
9	0.0836	0.1204	-0.0725	0.3815	-0.2007	0.177	-0.1054	0.1405	-0.1078	-0.1447	0.0577	-0.1893	0.167	0.1552	0.042	0.1392	0.0006	0.0389	0.2975	0.0023	0.1994	79.6708	-26.1976	20.3956
10	0.7059	-0.0059	-0.0149	0.8855	-0.0509	0.7599	-0.0135	-0.1027	0.0806	-0.0703	0.0137	-0.1988	-0.0608	0.2699	0.0094	0.1115	-0.0435	0.0254	0.3194	0.0009	0.1975	87.4708	-8.6091	20.1545
11	1.2852	-0.0414	0.2036	1.7069	0.4066	0.9149	0.0135	0.2147	-0.2625	-0.004	-0.1124	0.1696	0.2331	-0.0502	0.065	0.2177	-0.0427	0.026	0.2421	-0.0321	0.2336	57.7901	-46.2067	23.7532
12	0.8425	-0.0113	-0.1492	0.6772	0.121	0.5407	-0.047	0.0949	-0.0902	0.0465	-0.0547	0.3457	0.0957	-0.21	0.0545	0.138	-0.0697	0.0328	0.3161	-0.0409	0.3171	42.6458	-27.0063	29.7051
13	0.393	0.3075	0.1305	0.9415	-0.5731	0.6941	0.0375	-0.2059	0.1853	0.2362	0.0863	-0.3573	-0.1921	0.2537	-0.0962	0.4388	-0.0389	-0.0522	0.4336	-0.0374	0.3401	70.3498	-11.9619	50.3736
14	0.0206	-0.0771	0.0193	0.4406	-0.0536	0.02	0.0931	-0.2771	0.1685	0.2417	0.0038	0.1833	-0.0573	-0.2856	0.0198	0.3812	0.0481	-0.0353	0.3846	-0.0601	0.3133	59.2874	4.2622	36.5815
15	0.8849	-1.0585	-1.2951	2.0894	0.5827	3.0349	-0.047	0.0723	-0.1076	-0.1878	0.0482	-0.3015	0.1838	0.115	-0.0225	0.3629	-0.0289	0.0769	0.2663	0.0058	0.3722	72.2039	-22.1781	7.8666
16	0.7564	0.8464	0.6624	1.6639	0.1053	1.1442	0.1751	0.3515	-0.1747	-0.2459	-0.192	0.2794	0.0725	-0.2088	0.1044	0.3203	-0.1004	0.0282	0.465	-0.0816	0.3813	57.0077	-36.1416	19.8103

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 165 )	A	0
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 166 through 218 )	A	0
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 219 through 331 )	A	0
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 149 )	B	0
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 150 through 331 )	B	0
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 2 through 46 )	C	0
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 47 through 84 )	C	0
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 85 through 178 )	C	0
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 179 through 225 )	C	0
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 226 through 331 )	C	0
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 1 through 129 )	D	0
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 130 through 331 )	D	0
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 400 )	A	400
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 400 )	B	400
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 400 )	C	400
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 400 )	D	400

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