PDB-5ld5: Crystal structure of a bacterial dehydrogenase at 2.19 Angstroms ...

ID or keywords:

Entry

Database: PDB / ID: 5ld5

Title

Crystal structure of a bacterial dehydrogenase at 2.19 Angstroms resolution

Components

Glyceraldehyde-3-phosphate dehydrogenase

Glyceraldehyde 3-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE / Atopobium vaginae /

GAPDH / NAD /

dehydrogenase

Function / homology

Function and homology information

Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / glucose metabolic process / NAD binding /

NADP binding
Similarity search - Function

Biological species

Atopobium vaginae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1906 Å

Authors

Querol-Garcia, J. / Fernandez, F.J. / Gomez, S. / Fulla, D. / Juanhuix, J. / Vega, M.C.

Funding support

Spain,

Belgium, 4items

Organization	Grant number	Country
Spanish Ministry of Economy and Competitiveness	CTQ2015-66206-C2-2-R	Spain
Instituto de Salud Carlos III	PI12/01667	Spain
Regional Government of Madrid	S2010/BD-2316	Spain
European Union	ComplexINC (Contract No. 279039)	Belgium

Citation

Journal: Front Microbiol / Year: 2017
Title: Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen A. vaginae, an Immunoevasive Factor that Interacts with the Human C5a Anaphylatoxin.
Authors: Querol-Garcia, J. / Fernandez, F.J. / Marin, A.V. / Gomez, S. / Fulla, D. / Melchor-Tafur, C. / Franco-Hidalgo, V. / Alberti, S. / Juanhuix, J. / Rodriguez de Cordoba, S. / Regueiro, J.R. / Vega, M.C.

History

Deposition	Jun 23, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 12, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ld5.cif.gz	538.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5ld5.ent.gz	447 KB	Display	PDB format
PDBx/mmJSON format	5ld5.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/ld/5ld5 ftp://data.pdbj.org/pub/pdb/validation_reports/ld/5ld5	HTTPS FTP

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Related structure data

Similar structure data	3lvf-d 6ynf-2 6fzh-1 6m61-d 3lc7-d 4boy-1 6ynd-2 3pym-1 4qx6-d 2d2i-1 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 (9)

Deposited unit

A: Glyceraldehyde-3-phosphate dehydrogenase

B: Glyceraldehyde-3-phosphate dehydrogenase

C: Glyceraldehyde-3-phosphate dehydrogenase

D: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

158 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)	71.390, 132.110, 85.320
Angle α, β, γ (deg.)	90.00, 104.88, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase Mass: 38461.613 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Atopobium vaginae (bacteria) / Gene: gap, HMPREF0091_11005 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rossetta pLysS References: UniProt: F1T6A5, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.43 Å³/Da / Density % sol: 49.3 % / Description: Plate or cube-shaped crystals
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M sodium citrate pH 5.5, 20% PEG 3000 / PH range: 5.0 - 6.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2015
Radiation	Monochromator: Channel-cut Si(111) + KB focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.1906→47.714 Å / Num. obs: 77410 / % possible obs: 99 % / Redundancy: 6.7 % / B_iso Wilson estimate: 37.96 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.1157 / Net I/σ(I): 9.46
Reflection shell	Resolution: 2.191→2.269 Å / Redundancy: 6.4 % / R_merge(I) obs: 0.8224 / Mean I/σ(I) obs: 2.01 / % possible all: 90

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Processing

Software

Name	Version	Classification
XDS	March 1, 2015	data reduction
Aimless	0.5.26	data scaling
PHENIX	1.9_1692	refinement
PHASER	2.6.1	phasing
Coot	0.8.2	model building

Refinement

Method to determine structure:

SAD / Resolution: 2.1906→47.714 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / Phase error: 28.09

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2266	3864	5 %	Random selection
R_work	0.1773	-	-	-
obs	0.1797	77208	98.45 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 37.96 Å²

Refinement step

Cycle: LAST / Resolution: 2.1906→47.714 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10290	0	248	325	10863

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	10798
X-RAY DIFFRACTION	f_angle_d	1.097	14679
X-RAY DIFFRACTION	f_dihedral_angle_d	13.144	3935
X-RAY DIFFRACTION	f_chiral_restr	0.044	1698
X-RAY DIFFRACTION	f_plane_restr	0.005	1877

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 (%)
2.1906-2.2173	0.389	94	0.3502	1782	X-RAY DIFFRACTION	68
2.2173-2.2454	0.3308	142	0.2707	2688	X-RAY DIFFRACTION	99
2.2454-2.2749	0.2753	136	0.2615	2584	X-RAY DIFFRACTION	99
2.2749-2.3061	0.2929	140	0.2532	2664	X-RAY DIFFRACTION	100
2.3061-2.339	0.2958	139	0.2558	2628	X-RAY DIFFRACTION	100
2.339-2.3739	0.3096	140	0.2379	2655	X-RAY DIFFRACTION	100
2.3739-2.411	0.2691	137	0.2393	2602	X-RAY DIFFRACTION	100
2.411-2.4506	0.3061	141	0.2265	2682	X-RAY DIFFRACTION	100
2.4506-2.4928	0.2865	139	0.2328	2639	X-RAY DIFFRACTION	100
2.4928-2.5381	0.3099	140	0.2229	2645	X-RAY DIFFRACTION	100
2.5381-2.587	0.2942	139	0.2261	2644	X-RAY DIFFRACTION	100
2.587-2.6398	0.2956	138	0.2154	2646	X-RAY DIFFRACTION	100
2.6398-2.6971	0.2627	140	0.2164	2642	X-RAY DIFFRACTION	100
2.6971-2.7599	0.3132	141	0.1995	2669	X-RAY DIFFRACTION	100
2.7599-2.8289	0.2479	138	0.2023	2637	X-RAY DIFFRACTION	100
2.8289-2.9054	0.2566	139	0.1994	2633	X-RAY DIFFRACTION	100
2.9054-2.9908	0.2781	140	0.1997	2658	X-RAY DIFFRACTION	100
2.9908-3.0874	0.2527	141	0.204	2666	X-RAY DIFFRACTION	100
3.0874-3.1977	0.2512	139	0.1923	2636	X-RAY DIFFRACTION	100
3.1977-3.3257	0.2133	139	0.1797	2637	X-RAY DIFFRACTION	100
3.3257-3.477	0.2359	141	0.1724	2671	X-RAY DIFFRACTION	100
3.477-3.6603	0.2199	140	0.1714	2657	X-RAY DIFFRACTION	100
3.6603-3.8895	0.1868	140	0.1547	2656	X-RAY DIFFRACTION	100
3.8895-4.1896	0.1882	141	0.1424	2685	X-RAY DIFFRACTION	100
4.1896-4.6109	0.1628	139	0.1247	2633	X-RAY DIFFRACTION	100
4.6109-5.2774	0.1689	141	0.1334	2683	X-RAY DIFFRACTION	100
5.2774-6.6461	0.2082	141	0.1535	2670	X-RAY DIFFRACTION	100
6.6461-47.714	0.1725	139	0.1445	2652	X-RAY DIFFRACTION	97

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	1.3334	0.226	-0.1585	2.6595	0.8766	1.3415	-0.0179	0.0622	0.0139	-0.3609	0.1265	-0.2688	-0.2498	0.2575	-0.1118	0.4564	-0.0606	0.0863	0.3702	-0.095	0.3607	19.5707	-19.6834	4.6034
2	1.3093	-0.3402	-0.6776	2.2354	-0.3863	1.5056	-0.0791	0.0257	-0.0312	-0.1838	0.1847	-0.2258	0.1149	0.1565	-0.0874	0.3816	-0.0306	0.0503	0.3392	-0.1135	0.3257	15.9067	-40.8426	5.7708
3	0.6443	-0.22	-0.1296	1.1224	-0.2136	1.1421	0.0233	0.1169	-0.0929	-0.6507	0.0443	0.1208	0.2613	-0.0141	-0.05	0.3979	-0.0275	-0.0072	0.2632	-0.0031	0.244	-2.0949	-37.0763	11.9499
4	1.1458	-0.3455	-0.5229	1.6833	0.3721	1.8765	-0.0946	-0.1746	-0.1796	0.3335	0.1451	-0.0945	0.3215	0.2568	-0.0347	0.3784	0.0726	-0.0442	0.292	-0.0132	0.2656	9.3262	-41.5778	23.5594
5	0.6885	0.2753	-0.1748	2.0703	-0.4706	1.8694	-0.0639	0.4228	0.0475	-0.6485	0.023	0.3029	-0.275	-0.2142	0.0344	0.6781	-0.0125	-0.2156	0.5364	0.0547	0.5347	-21.4421	-15.9951	-6.4148
6	0.5185	-0.2086	-0.3352	1.6134	0.1431	0.8755	0.034	0.1392	0.0731	-0.5693	0.0647	0.5064	-0.2408	-0.2125	-0.0872	0.5449	0.0174	-0.0856	0.3337	0.065	0.4569	-15.4859	2.8416	11.0309
7	1.2607	0.1002	-0.5209	1.3295	-1.2937	1.4533	-0.0792	0.046	0.2997	-0.0252	-0.0199	0.5849	-0.0071	-0.4919	0.101	0.3018	-0.02	0.0214	0.4512	-0.027	0.6372	-32.2232	-17.3722	33.8168
8	0.6989	-0.579	0.3769	1.3378	0.7992	1.8311	0.09	-0.2626	0.0427	0.4877	-0.2191	0.2435	0.3064	-0.4237	0.1241	0.4483	-0.0988	0.1574	0.4953	0.036	0.5424	-30.4989	-34.2467	42.6315
9	0.5866	0.6348	-0.0305	0.9141	0.194	0.3206	-0.0553	0.0301	0.0635	0.1637	0.1161	0.5676	0.2696	-0.075	-0.0432	0.4172	-0.0325	0.0515	0.327	0.0505	0.4526	-12.7374	-38.2024	29.6442
10	1.1818	0.1729	-0.5273	0.9171	-0.5314	1.4123	0.0324	0.1009	-0.0033	-0.1521	-0.0104	0.2842	0.1952	-0.2792	-0.007	0.3072	-0.0932	-0.0296	0.3223	0.0001	0.4501	-20.4188	-40.8692	19.1759
11	1.1382	-0.3804	0.1444	1.9668	0.9896	2.4855	-0.1351	-0.1312	0.0306	0.4689	0.1352	-0.1807	0.1207	0.289	-0.0216	0.3641	0.0495	-0.0398	0.3691	-0.0279	0.2492	10.8975	-20.0145	43.8678
12	1.1622	-0.5696	-0.2987	2.5789	-0.5959	1.934	-0.0516	-0.4499	0.115	0.6618	0.1823	-0.1529	-0.145	0.1178	-0.122	0.4443	0.0472	-0.0557	0.4138	-0.0768	0.2816	5.3643	-3.5919	51.312
13	0.8996	-0.3405	-0.0519	1.2847	0.3845	1.4599	0.0961	-0.089	0.1125	0.3291	0.0523	0.1417	-0.2556	0.0004	-0.169	0.3394	0.0074	0.0275	0.2676	0.0019	0.263	-4.0797	1.184	30.1263
14	1.3665	-0.3736	-0.0624	1.9373	-0.0276	1.4918	-0.0172	-0.0117	0.2111	-0.3614	0.1296	-0.3017	-0.2622	0.2285	-0.1235	0.3597	-0.0859	0.0593	0.3049	-0.0547	0.3064	9.3217	3.7926	25.6923

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 119 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 120 through 183 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 184 through 267 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 268 through 355 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 16 through 136 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 137 through 355 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 15 through 93 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 94 through 167 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 168 through 244 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 245 through 356 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 16 through 92 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 93 through 167 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 168 through 267 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 268 through 355 )

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