PDB-5t73: Crystal structure of S.aureus glyceraldehyde-3-phosphate-dehydrog...

ID or keywords:

Entry

Database: PDB / ID: 5t73

Title

Crystal structure of S.aureus glyceraldehyde-3-phosphate-dehydrogenase (Gap) containing oxidized Cys151

Components

Glyceraldehyde-3-phosphate dehydrogenase 1

Glyceraldehyde 3-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE /

Glycolysis /

Oxidation

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 /

cytoplasm
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.599 Å

Authors

Pietrzyk-Brzezinska, A.J. / Wahl, M.C.

Citation

Journal: Antioxid. Redox Signal. / Year: 2018
Title: Protein S-Bacillithiolation Functions in Thiol Protection and Redox Regulation of the Glyceraldehyde-3-Phosphate Dehydrogenase Gap in Staphylococcus aureus Under Hypochlorite Stress.
Authors: Imber, M. / Huyen, N.T.T. / Pietrzyk-Brzezinska, A.J. / Loi, V.V. / Hillion, M. / Bernhardt, J. / Tharichen, L. / Kolsek, K. / Saleh, M. / Hamilton, C.J. / Adrian, L. / Grater, F. / Wahl, M.C. / Antelmann, H.

History

Deposition	Sep 2, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 28, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 25, 2017	Group: Database references
Revision 1.2	Feb 7, 2018	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.3	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5t73.cif.gz	509.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5t73.ent.gz	424.9 KB	Display	PDB format
PDBx/mmJSON format	5t73.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/t7/5t73 ftp://data.pdbj.org/pub/pdb/validation_reports/t7/5t73	HTTPS FTP

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Related structure data

Related structure data	3lc7S S: Starting model for refinement
Similar structure data	5jyf-d 5v8y-1 6iep-d 1obf-1 2x5k-d 1j0x-d 1crw-1 6iq6-2 6ynh-d 3lc1-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 (10)

Deposited unit

A: Glyceraldehyde-3-phosphate dehydrogenase 1

B: Glyceraldehyde-3-phosphate dehydrogenase 1

C: Glyceraldehyde-3-phosphate dehydrogenase 1

D: Glyceraldehyde-3-phosphate dehydrogenase 1

hetero molecules

146 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	95.692, 111.456, 128.063
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Glyceraldehyde-3-phosphate dehydrogenase 1 / Glyceraldehyde 3-phosphate dehydrogenase / GAPDH 1 / NAD-dependent glyceraldehyde-3-phosphate dehydrogenase Mass: 36368.762 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain MRSA252) (bacteria) Strain: MRSA252 / Gene: gapA1, gap, gapA, SAR0828 / Production host: Escherichia coli (E. coli) References: UniProt: Q6GIL8, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.59 Å³/Da / Density % sol: 52.5 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30 % (w/v) PEG 3350, 0.1 M Tris, pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.976 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.599→48.157 Å / Num. obs: 42806 / % possible obs: 99.8 % / Redundancy: 7.4 % / CC_1/2: 0.989 / R_merge(I) obs: 0.246 / Net I/σ(I): 8.68
Reflection shell	Resolution: 2.599→2.65 Å / Redundancy: 7.4 % / R_merge(I) obs: 1.23 / Mean I/σ(I) obs: 1.61 / CC_1/2: 0.56 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3lc7

3lc7

Resolution: 2.599→48.157 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.83

	R_factor	Num. reflection	% reflection
R_free	0.2604	2098	4.9 %
R_work	0.1967	-	-
obs	0.2	42794	99.79 %

Solvent computation

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

Displacement parameters

B_iso mean: 38.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.599→48.157 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10164	0	8	213	10385

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	10330
X-RAY DIFFRACTION	f_angle_d	1.111	14003
X-RAY DIFFRACTION	f_dihedral_angle_d	15.258	3783
X-RAY DIFFRACTION	f_chiral_restr	0.051	1640
X-RAY DIFFRACTION	f_plane_restr	0.006	1833

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 (%)
2.5985-2.659	0.3688	135	0.2869	2633	X-RAY DIFFRACTION	98
2.659-2.7254	0.378	138	0.2729	2668	X-RAY DIFFRACTION	100
2.7254-2.7991	0.389	138	0.2735	2668	X-RAY DIFFRACTION	100
2.7991-2.8815	0.3392	138	0.2697	2691	X-RAY DIFFRACTION	100
2.8815-2.9745	0.3206	138	0.266	2667	X-RAY DIFFRACTION	100
2.9745-3.0808	0.3125	140	0.2515	2716	X-RAY DIFFRACTION	100
3.0808-3.2041	0.3031	139	0.2405	2691	X-RAY DIFFRACTION	100
3.2041-3.3499	0.3081	138	0.2242	2682	X-RAY DIFFRACTION	100
3.3499-3.5264	0.2825	139	0.2069	2696	X-RAY DIFFRACTION	100
3.5264-3.7473	0.2822	140	0.1907	2709	X-RAY DIFFRACTION	100
3.7473-4.0365	0.2138	141	0.1679	2725	X-RAY DIFFRACTION	100
4.0365-4.4425	0.2162	141	0.1475	2735	X-RAY DIFFRACTION	100
4.4425-5.0847	0.2106	142	0.1396	2748	X-RAY DIFFRACTION	100
5.0847-6.4038	0.2104	143	0.165	2785	X-RAY DIFFRACTION	100
6.4038-48.1651	0.1981	148	0.1703	2882	X-RAY DIFFRACTION	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	1.8764	-0.3038	-0.5991	2.3523	1.0406	1.2768	0.0131	0.1462	-0.1437	-0.2014	-0.0512	0.2412	0.1644	-0.3436	0.0404	0.4799	-0.097	-0.0579	0.4399	0.011	0.3076	-10.2974	37.1494	1.2172
2	3.6423	-2.1001	1.3831	1.5498	0.3211	4.3365	0.0141	-0.2836	-1.0251	-0.7013	0.1455	-1.4844	0.7336	0.7688	-0.2105	0.6859	-0.1391	-0.0188	0.3954	0.0181	0.619	9.1982	31.2047	-9.3588
3	-0.0448	-0.1704	0.2497	0.5477	-0.0236	1.5108	-0.0622	-0.0268	-0.1595	-0.1519	0.0598	-0.0764	0.1156	0.1245	0.041	0.3715	0.0336	0.0123	0.3377	-0.0278	0.38	10.7432	42.2496	7.2603
4	1.8348	-1.3349	0.0408	3.4642	-1.0504	3.2839	0.0486	0.0343	0.1187	-0.1858	-0.0878	0.2626	0.3478	-0.1365	0.1373	0.3333	-0.02	0.029	0.2998	-0.0198	0.3495	4.6759	46.2779	24.4259
5	1.9976	-1.0399	-0.4563	4.2718	1.7887	2.4942	0.0969	0.1089	-0.7847	-0.1138	0.4782	-0.2606	1.0989	-0.3602	-0.2012	0.6419	0.0221	0.2131	0.4382	0.0561	0.6952	13.2112	39.3388	13.4796
6	1.5641	-0.4048	0.3367	1.2576	0.1835	1.614	0.0595	-0.1131	-0.0848	-0.138	0.0731	-0.195	0.2403	0.1063	-0.085	0.4233	-0.0157	0.0428	0.3323	-0.0369	0.3789	17.0987	43.3736	6.8987
7	5.2808	0.6583	-2.0453	6.0852	1.0765	4.1652	0.2107	0.9365	0.0088	-0.6328	-0.5324	-0.6816	-0.2684	0.5433	0.2813	0.3746	-0.032	0.0556	0.6022	0.0052	0.5183	28.7593	53.2415	-4.369
8	1.8112	0.8799	-0.5134	1.7289	-0.1083	0.7938	-0.1514	0.263	0.031	-0.4456	0.2515	0.0072	-0.1019	0.1575	-0.1104	0.3923	-0.0419	0.0348	0.3397	-0.0344	0.3549	11.9939	49.9153	-1.3001
9	2.5783	0.3845	0.5218	1.0805	0.3227	1.5725	-0.2254	-0.2798	0.1212	0.1064	0.143	-0.0105	-0.2172	-0.1336	0.0264	0.4782	-0.0341	-0.025	0.3403	-0.0175	0.3581	14.7047	76.2734	36.237
10	1.91	0.7085	0.0528	8.9042	1.3366	3.2288	-0.3107	-0.7391	0.5722	1.3444	-0.4949	1.2764	-0.3707	-0.6086	0.4968	0.5517	0.07	-0.0869	0.3901	-0.1217	0.5321	6.7486	78.589	42.747
11	1.602	-0.9504	-0.2072	2.9687	1.3689	0.9028	-0.0119	0.0596	0.4004	-0.1614	0.1711	-0.2917	-0.5054	0.3831	-0.1232	0.6192	-0.0831	-0.0147	0.4512	0.0127	0.4111	26.8087	80.6431	32.6657
12	0.6757	-0.3003	0.1979	0.8685	-0.17	0.641	0.131	0.0631	0.0316	-0.0508	-0.1286	-0.1225	-0.1179	0.3633	-0.0376	0.4023	-0.0091	0.0508	0.4251	-0.0265	0.4135	25.606	62.4347	21.1659
13	6.8511	-0.2988	-0.1352	4.0293	-1.3751	2.6865	0.0604	-1.6332	0.2603	0.5635	-0.2664	-1.0397	-1.2079	0.4999	0.1942	0.6396	-0.0742	0.1011	0.5431	0.0673	0.4249	15.0258	74.0254	7.9405
14	2.4967	-0.0389	0.3475	0.9103	0.3194	1.2684	-0.0173	-0.0942	-0.045	-0.0451	0.0019	-0.2737	-0.0967	0.1349	0.0213	0.3103	-0.0151	0.0132	0.3427	0.03	0.4117	24.4823	55.1295	18.1811
15	2.0099	-1.1189	0.0677	6.3752	-5.0363	4.4098	0.2753	-0.2694	0.2696	0.8981	0.1323	-0.5286	-0.6598	-0.2784	-0.0064	0.5129	-0.1193	0.0553	0.6747	-0.0056	0.358	27.4825	55.1739	35.4273
16	1.2519	-0.4719	-0.1374	1.3129	0.8343	1.3648	0.0114	-0.1107	-0.1634	0.0129	0.0859	-0.0849	-0.088	0.172	-0.0537	0.3224	-0.0024	0.0384	0.3274	0.0005	0.3477	22.7811	54.6133	27.9966
17	1.5658	0.0513	-0.1229	1.7975	-1.0043	1.7819	0.0693	0.2285	0.0759	-0.3263	0.0261	0.2291	-0.0523	0.1937	-0.0203	0.5142	-0.0592	-0.027	0.3864	-0.0154	0.3618	-1.2577	75.192	-3.33
18	5.635	1.2395	-0.8379	4.9458	-1.5548	5.2828	0.2251	1.1021	-0.7752	-0.5094	-0.4119	-0.2461	0.3419	0.8619	0.087	0.5529	-0.0124	-0.0431	0.5713	-0.0891	0.4573	4.6754	69.0541	-9.3547
19	0.8686	0.0648	0.1479	0.5849	-0.2845	0.723	-0.0854	0.0648	0.2732	-0.1779	0.136	0.2661	-0.4394	-0.1325	-0.0505	0.6098	0.0586	-0.0341	0.4013	0.0327	0.49	-10.6519	84.1096	3.887
20	2.9818	1.2416	-0.5439	3.6221	-0.3161	3.1441	0.0373	-0.0894	0.1796	-0.452	-0.1964	0.2471	-1.072	-0.2489	0.1053	0.4815	0.0736	0.0185	0.3904	0.0225	0.3479	-2.3454	76.0202	24.1789
21	2.0098	1.0652	0.0391	3.4329	-0.1986	5.0493	0.0786	-0.4504	0.2574	0.3769	-0.3071	0.0171	-1.043	-0.5668	0.1676	0.6446	0.173	0.2009	0.5791	0.1464	0.6487	-23.6646	85.4532	14.924
22	2.7353	0.1633	0.1647	0.9822	-0.0758	1.739	-0.1189	0.1052	0.438	-0.0089	0.1359	0.3947	-0.4104	-0.0775	-0.0422	0.4184	0.0761	-0.0339	0.4214	0.1361	0.5119	-19.7965	73.4473	20.2031
23	5.9611	-0.0973	-0.5206	7.1165	-1.2102	2.1573	0.3517	0.5476	0.0759	0.08	0.5692	1.6162	-0.3445	-0.8035	-0.6012	0.3984	0.1568	0.0297	0.7839	0.2051	0.8676	-37.1061	66.4548	17.1558
24	1.5415	-0.4813	-0.2036	2.1075	-0.5524	1.2761	-0.1168	0.111	0.0173	-0.2637	0.1199	0.4122	0.0666	-0.4286	-0.0969	0.3289	0.0476	-0.045	0.4245	0.0538	0.4946	-21.9664	69.51	9.4109
25	0.7306	0.1138	-0.7899	1.599	0.0834	2.9622	-0.0512	-0.2775	0.1753	0.3765	0.481	0.1337	-0.0577	-0.0985	-0.3165	0.3637	0.0873	-0.0142	0.4166	0.0503	0.3547	-3.2572	48.5252	45.0963
26	3.62	1.8084	-0.9721	4.1379	-1.5241	6.1366	-0.2484	-1.4151	0.4377	0.6095	0.6484	-0.6864	-0.0953	1.0393	-0.2334	0.6845	0.0571	0.1402	0.7914	-0.1094	0.4115	-0.7088	53.6092	54.2237
27	0.9257	-0.5916	-0.7099	1.3645	-0.3323	2.0524	-0.0023	-0.1365	-0.0942	-0.0774	0.0235	0.0856	0.1337	0.4093	-0.0624	0.4588	0.0048	0.0209	0.4159	-0.0188	0.3246	3.292	45.6897	38.339
28	2.5115	-2.0404	1.1835	6.1438	-1.1024	4.8926	-0.0287	-0.1291	-0.8765	0.7422	-0.4862	-1.1849	0.3098	1.0491	0.5458	0.6926	0.2171	0.1023	0.5197	0.2236	0.8269	10.4452	40.1654	44.8718
29	0.5618	-0.17	-0.19	0.9823	0.0829	2.1886	0.0803	-0.1058	-0.1473	0.2667	0.0243	0.1764	0.0156	-0.3962	-0.1078	0.3941	-0.0271	0.0123	0.4138	0.0397	0.4137	-14.6499	49.7081	43.3973
30	4.209	0.991	-0.2578	3.381	0.945	2.7969	-0.0604	-0.4947	0.2452	0.4137	-0.1603	0.2025	0.545	-0.2374	0.4027	0.3032	0.0407	-0.0142	0.4031	-0.069	0.4008	-13.8273	52.9456	18.8557
31	3.6744	-0.4256	-0.6035	3.5884	0.9476	4.2434	-0.3302	1.2149	-0.4519	1.2148	-0.4119	-0.2409	0.3452	-0.1921	0.4508	0.4346	0.135	0.0813	0.6982	0.0699	0.7263	-22.8111	57.7665	30.2811
32	0.6641	0.0608	-0.1289	0.756	-0.4716	1.5222	0.046	-0.0789	0.2496	0.1526	0.0528	0.132	-0.3163	-0.2548	-0.0854	0.4818	0.0725	0.1067	0.4069	0.023	0.45	-16.1732	69.0832	38.7524

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:135)
2	X-RAY DIFFRACTION	2	(chain A and resid 136:140)
3	X-RAY DIFFRACTION	3	(chain A and resid 141:191)
4	X-RAY DIFFRACTION	4	(chain A and resid 192:208)
5	X-RAY DIFFRACTION	5	(chain A and resid 209:215)
6	X-RAY DIFFRACTION	6	(chain A and resid 216:251)
7	X-RAY DIFFRACTION	7	(chain A and resid 252:261)
8	X-RAY DIFFRACTION	8	(chain A and resid 262:335)
9	X-RAY DIFFRACTION	9	(chain B and resid 2:52)
10	X-RAY DIFFRACTION	10	(chain B and resid 53:62)
11	X-RAY DIFFRACTION	11	(chain B and resid 63:137)
12	X-RAY DIFFRACTION	12	(chain B and resid 138:191)
13	X-RAY DIFFRACTION	13	(chain B and resid 192:196)
14	X-RAY DIFFRACTION	14	(chain B and resid 197:266)
15	X-RAY DIFFRACTION	15	(chain B and resid 267:271)
16	X-RAY DIFFRACTION	16	(chain B and resid 272:335)
17	X-RAY DIFFRACTION	17	(chain C and resid 2:52)
18	X-RAY DIFFRACTION	18	(chain C and resid 53:62)
19	X-RAY DIFFRACTION	19	(chain C and resid 63:191)
20	X-RAY DIFFRACTION	20	(chain C and resid 192:211)
21	X-RAY DIFFRACTION	21	(chain C and resid 212:225)
22	X-RAY DIFFRACTION	22	(chain C and resid 226:251)
23	X-RAY DIFFRACTION	23	(chain C and resid 252:262)
24	X-RAY DIFFRACTION	24	(chain C and resid 263:335)
25	X-RAY DIFFRACTION	25	(chain D and resid 2:22)
26	X-RAY DIFFRACTION	26	(chain D and resid 23:28)
27	X-RAY DIFFRACTION	27	(chain D and resid 29:56)
28	X-RAY DIFFRACTION	28	(chain D and resid 57:62)
29	X-RAY DIFFRACTION	29	(chain D and resid 63:191)
30	X-RAY DIFFRACTION	30	(chain D and resid 192:208)
31	X-RAY DIFFRACTION	31	(chain D and resid 209:215)
32	X-RAY DIFFRACTION	32	(chain D and resid 216:335)

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