PDB-7jwk: Crystal Structure of Glyceraldehyde-3-phosphate Dehydrogenase (GA...

ID or keywords:

Entry

Database: PDB / ID: 7jwk

Title

Crystal Structure of Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) from Mycoplasma genitalium with bound NAD

Components

Glyceraldehyde-3-phosphate dehydrogenase

Glyceraldehyde 3-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID /

dehydrogenase /

GAPDH / NAD /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

glycosylation-dependent protein binding / NADH regeneration / adhesion of symbiont to host cell /

glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding /

NADP binding /

cell surface /

cytoplasm
Similarity search - Function

Biological species

Mycoplasma genitalium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) from Mycoplasma genitalium with bound NAD
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Aug 25, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 9, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7jwk.cif.gz	526.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7jwk.ent.gz	433.2 KB	Display	PDB format
PDBx/mmJSON format	7jwk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jw/7jwk ftp://data.pdbj.org/pub/pdb/validation_reports/jw/7jwk	HTTPS FTP

-
Related structure data

Related structure data	5vmtS S: Starting model for refinement
Similar structure data	3vaz-1 3vaz-3 3vaz-2 3p20-d 6aaj-d 7a8w-d 5udj-d 3sth-1 5do9-6 5udk-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

-
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

B: Glyceraldehyde-3-phosphate dehydrogenase

C: Glyceraldehyde-3-phosphate dehydrogenase

D: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

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

1

A: Glyceraldehyde-3-phosphate dehydrogenase

B: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration
77.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Glyceraldehyde-3-phosphate dehydrogenase

D: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

defined by author&software
77.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	91.600, 94.170, 172.800
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase / GAPDH / NAD-dependent glyceraldehyde-3-phosphate dehydrogenase Mass: 37663.234 Da / Num. of mol.: 4 / Fragment: MygeA.00914.a.B2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195) (bacteria) Strain: ATCC 33530 / G-37 / NCTC 10195 / Gene: gapA, gap, MG301 / Plasmid: MygeA.00914.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P47543, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.27 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: MygeA.00914.a.B2.PW38693 at 18 mg/ml incubated with 3 mM glycerol-3-phosphate and NAD, then mixed 1:1 with MorpheusII(f11): 10%(w/v) PEG 8K, 20%(w/v) 1,5-pentanediol, 0.1 M GlyGly/AMPD pH 8. ...Details: MygeA.00914.a.B2.PW38693 at 18 mg/ml incubated with 3 mM glycerol-3-phosphate and NAD, then mixed 1:1 with MorpheusII(f11): 10%(w/v) PEG 8K, 20%(w/v) 1,5-pentanediol, 0.1 M GlyGly/AMPD pH 8.5, 0.02 M of each xylitol, D-(--fructose, D-sorbitol, myo-inositol, L-rhamnose monohydrate. Tray: 312789f11. Puck: pvq3-6.

Crystal

Density Matthews: 2.47 Å³/Da / Density % sol: 50.27 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MygeA.00914.a.B2.PW38693 at 18 mg/ml incubated with 3 mM glycerol-3-phosphate and NAD, then mixed 1:1 with MorpheusII(f11): 10%(w/v) PEG 8K, 20%(w/v) 1,5-pentanediol, 0.1 M GlyGly/AMPD pH 8. ...

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

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

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 19, 2020 / Details: Beryllium Lenses

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→45.43 Å / Num. obs: 76513 / % possible obs: 99.9 % / Redundancy: 7.134 % / B_iso Wilson estimate: 47.822 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.081 / R_rim(I) all: 0.087 / Χ²: 1.009 / Net I/σ(I): 14.58 / Num. measured all: 545819 / Scaling rejects: 4

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.2-2.26	7.223	0.576	3.62	40206	5568	5566	0.91	0.62	100
2.26-2.32	7.221	0.482	4.25	39393	5456	5455	0.933	0.518	100
2.32-2.39	7.224	0.365	5.36	38419	5318	5318	0.96	0.393	100
2.39-2.46	7.226	0.323	5.98	37168	5144	5144	0.966	0.348	100
2.46-2.54	7.221	0.265	7.04	36337	5032	5032	0.974	0.286	100
2.54-2.63	7.222	0.216	8.39	34924	4836	4836	0.985	0.233	100
2.63-2.73	7.22	0.172	10.38	33528	4645	4644	0.989	0.185	100
2.73-2.84	7.212	0.139	12.48	32697	4533	4534	0.992	0.149	100
2.84-2.97	7.192	0.118	14.52	31179	4335	4335	0.993	0.127	100
2.97-3.11	7.18	0.092	17.58	29683	4134	4134	0.995	0.099	100
3.11-3.28	7.152	0.081	19.88	28458	3981	3979	0.996	0.087	99.9
3.28-3.48	7.118	0.075	22.1	26513	3727	3725	0.996	0.081	99.9
3.48-3.72	7.103	0.069	23.47	25052	3528	3527	0.996	0.075	100
3.72-4.02	7.05	0.064	25.33	23299	3305	3305	0.996	0.069	100
4.02-4.4	7.03	0.058	27.83	21406	3045	3045	0.997	0.063	100
4.4-4.92	6.979	0.057	28.54	19305	2768	2766	0.997	0.062	99.9
4.92-5.68	6.954	0.058	28.61	17078	2457	2456	0.997	0.063	100
5.68-6.96	6.845	0.057	28.16	14394	2107	2103	0.997	0.062	99.8
6.96-9.84	6.668	0.055	29.41	11049	1661	1657	0.996	0.06	99.8
9.84-45.43	6.02	0.057	28.28	5731	972	952	0.996	0.063	97.9

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHENIX	1.18.2-3874	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5VMT

5vmt

Resolution: 2.2→45.43 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1966	4556	6.17 %
R_work	0.1585	69260	-
obs	0.1608	73816	96.44 %

Solvent computation

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

Displacement parameters

B_iso max: 120.73 Å² / B_iso mean: 51.8934 Å² / B_iso min: 22.38 Å²

Refinement step

Cycle: final / Resolution: 2.2→45.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9975	0	244	424	10643
B_iso mean	-	-	46.09	45.05	-
Num. residues	-	-	-	-	1323

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10423
X-RAY DIFFRACTION	f_angle_d	0.837	14245
X-RAY DIFFRACTION	f_chiral_restr	0.054	1726
X-RAY DIFFRACTION	f_plane_restr	0.006	1874
X-RAY DIFFRACTION	f_dihedral_angle_d	16.126	3782

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / 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 (%)
2.2-2.22	0.2389	140	0.2026	2108	2248	89
2.22-2.25	0.2887	135	0.2086	2126	2261	91
2.25-2.28	0.2457	152	0.1972	2152	2304	91
2.28-2.31	0.2644	115	0.1925	2191	2306	91
2.31-2.34	0.2508	139	0.1863	2183	2322	92
2.34-2.37	0.2151	180	0.1798	2133	2313	93
2.37-2.4	0.2089	142	0.1859	2258	2400	94
2.4-2.44	0.2562	164	0.186	2189	2353	93
2.44-2.48	0.2395	134	0.1782	2248	2382	95
2.48-2.52	0.2	155	0.1721	2225	2380	95
2.52-2.56	0.2364	142	0.1776	2261	2403	95
2.56-2.61	0.2282	143	0.1821	2308	2451	96
2.61-2.66	0.2541	153	0.1785	2262	2415	97
2.66-2.71	0.2242	174	0.1706	2312	2486	97
2.71-2.77	0.2067	131	0.1706	2335	2466	97
2.77-2.84	0.2101	139	0.1759	2318	2457	98
2.84-2.91	0.2163	144	0.1836	2343	2487	98
2.91-2.99	0.2293	157	0.1744	2365	2522	98
2.99-3.07	0.2136	194	0.1705	2302	2496	99
3.07-3.17	0.1856	155	0.1675	2364	2519	99
3.17-3.29	0.1968	169	0.1684	2373	2542	99
3.29-3.42	0.2335	141	0.1683	2375	2516	99
3.42-3.57	0.1915	145	0.1716	2386	2531	99
3.57-3.76	0.1734	154	0.1526	2421	2575	100
3.76-4	0.1899	157	0.1512	2398	2555	100
4-4.31	0.1744	151	0.1301	2409	2560	100
4.31-4.74	0.1491	147	0.119	2438	2585	100
4.74-5.42	0.1921	159	0.1377	2455	2614	100
5.42-6.83	0.176	162	0.1562	2459	2621	100
6.83-45.43	0.1705	183	0.1462	2563	2746	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	2.0948	-0.617	-0.9845	4.0545	-0.0529	3.3569	-0.0197	-0.1313	-0.4657	-0.0055	-0.0096	0.133	0.6041	0.1603	0.0418	0.3454	-0.0134	-0.066	0.243	0.0112	0.3286	23.0805	-26.9266	-20.5911
2	1.1891	0.0225	-0.2078	2.7755	0.329	1.7156	0.1117	0.3051	-0.168	-0.7835	-0.0369	-0.1232	0.1888	-0.0663	-0.0483	0.4384	0.0533	0.0318	0.3125	0.0102	0.2418	27.2521	-7.6247	-36.4482
3	1.3184	0.0193	-0.5753	1.8806	-0.4327	2.7183	0.1352	0.3166	-0.0683	-0.7955	-0.0073	0.0408	0.2117	-0.0252	-0.0861	0.4804	0.0572	-0.0277	0.3472	-0.0372	0.2161	24.6589	-11.7562	-39.4457
4	1.8807	-0.5254	-0.8116	3.8971	-0.7022	4.0894	0.2126	0.1905	0.5137	-0.2776	-0.0686	0.0229	-0.5876	-0.2885	-0.1527	0.3572	0.0548	0.1094	0.2992	0.0744	0.4246	21.7896	33.5274	-26.4373
5	1.3151	0.3198	-0.3827	2.9884	0.0541	1.0598	0.1242	0.1538	0.1837	-0.699	-0.0001	-0.5441	-0.1964	0.1506	-0.1446	0.4163	0.0328	0.2111	0.3452	0.0606	0.37	34.9209	13.4317	-34.9815
6	2.3788	-0.5432	-0.4274	2.1803	-0.2277	3.0091	-0.0362	-0.4548	-0.2334	0.856	-0.2037	-1.0041	-0.0041	0.6947	0.1148	0.5376	-0.0478	-0.2825	0.4915	0.0621	0.6077	41.9343	1.3329	2.3199
7	1.5117	0.1648	-0.1464	2.6222	-0.2637	1.7184	0.1096	-0.3759	0.1957	1.1231	0.0491	0.2333	-0.3029	-0.1339	-0.1162	0.6453	0.0213	0.1546	0.3895	0.0115	0.2379	16.4514	9.787	4.8281
8	6.4316	0.6433	-2.2991	0.7976	1.4438	4.7181	0.0064	-0.83	0.6162	1.0945	0.2079	-0.7032	-0.3441	0.438	-0.2009	0.7922	-0.0936	-0.203	0.409	-0.0771	0.4026	34.2191	11.599	8.871
9	2.2022	0.4555	-0.3957	0.2443	0.1168	2.6642	0.197	0.5223	0.1858	-0.7299	0.1078	1.2617	-0.3827	-0.736	-0.1183	0.4958	0.0655	-0.2862	0.7411	0.1748	1.0406	-6.954	6.5024	-33.8153
10	1.0983	0.4471	-1.3752	2.3006	0.271	2.0113	0.2256	0.0808	-0.0306	-0.2257	0.0009	1.4767	-0.31	-0.9362	-0.2245	0.2904	0.1349	0.2225	0.9307	0.2779	1.3631	-13.813	6.0743	-12.3996
11	1.0123	0.2663	-0.6744	0.435	-0.0049	1.0253	-0.0106	-0.0642	-0.0606	0.1536	0.1681	1.1	-0.2641	-0.4907	-0.2572	0.2717	0.0882	0.2171	0.4794	0.1187	0.6821	5.6068	13.2444	-11.1211
12	1.6453	0.0773	-0.9138	1.9159	-0.0482	1.6683	0.0731	-0.0621	-0.1355	0.4603	0.0906	1.0939	0.117	-0.4966	0.0651	0.3459	-0.0101	0.2383	0.5525	0.1348	0.7276	-1.9695	-1.9406	-5.0682

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 7 through 156 )	A	7 - 156
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 157 through 299 )	A	157 - 299
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 300 through 337 )	A	300 - 337
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 7 through 134 )	B	7 - 134
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 135 through 337 )	B	135 - 337
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 5 through 134 )	C	5 - 134
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 135 through 320 )	C	135 - 320
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 321 through 337 )	C	321 - 337
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 7 through 117 )	D	7 - 117
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 118 through 173 )	D	118 - 173
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 174 through 224 )	D	174 - 224
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 225 through 334 )	D	225 - 334

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi