PDB-9pg6: Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase fro...

ID or keywords:

Entry

Database: PDB / ID: 9pg6

Title

Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase from Bordetella pertussis (NAD bound)

Components

Glyceraldehyde-3-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Glyceraldehyde-3-phosphate 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

Bordetella pertussis Tohama I (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

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

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase from Bordetella pertussis (NAD bound)
Authors: Liu, L. / Ung, A.R. / Lovell, S. / Battaile, K.P.

History

Deposition	Jul 7, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9pg6.cif.gz	1012 KB	Display	PDBx/mmCIF format
PDB format	pdb9pg6.ent.gz	845.9 KB	Display	PDB format
PDBx/mmJSON format	9pg6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9pg6_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	9pg6_full_validation.pdf.gz	2.7 MB	Display
Data in XML	9pg6_validation.xml.gz	112.7 KB	Display
Data in CIF	9pg6_validation.cif.gz	141.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pg/9pg6 ftp://data.pdbj.org/pub/pdb/validation_reports/pg/9pg6	HTTPS FTP

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Related structure data

Similar structure data	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

E: Glyceraldehyde-3-phosphate dehydrogenase

F: Glyceraldehyde-3-phosphate dehydrogenase

G: Glyceraldehyde-3-phosphate dehydrogenase

H: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

304 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glyceraldehyde-3-phosphate dehydrogenase

B: Glyceraldehyde-3-phosphate dehydrogenase

C: Glyceraldehyde-3-phosphate dehydrogenase

D: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration
152 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Glyceraldehyde-3-phosphate dehydrogenase

F: Glyceraldehyde-3-phosphate dehydrogenase

G: Glyceraldehyde-3-phosphate dehydrogenase

H: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.826, 130.061, 140.967
Angle α, β, γ (deg.)	90.00, 90.86, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Glyceraldehyde-3-phosphate dehydrogenase Mass: 37360.496 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria) Gene: gap, hexC, BP1000 / Plasmid: BopeA.00052.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q7VZB9, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.12 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus A1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. BopeA.00052.a.B2.PW39379 at 12.4 mg/mL. 5mM NAD added to the protein prior ...Details: Morpheus A1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. BopeA.00052.a.B2.PW39379 at 12.4 mg/mL. 5mM NAD added to the protein prior to crystallization. plate 19841 well A1 drop 2, Puck: PSL-2110, Cryo: 80% crystallant + 20% PEG 200

Crystal

Density Matthews: 2.42 Å³/Da / Density % sol: 49.12 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus A1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. BopeA.00052.a.B2.PW39379 at 12.4 mg/mL. 5mM NAD added to the protein prior ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 25, 2025
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.15→49.03 Å / Num. obs: 153901 / % possible obs: 99.8 % / Redundancy: 7 % / CC_1/2: 0.996 / R_merge(I) obs: 0.184 / R_pim(I) all: 0.075 / R_rim(I) all: 0.199 / Χ²: 1.03 / Net I/σ(I): 7.8 / Num. measured all: 1076571
Reflection shell	Resolution: 2.15→2.21 Å / % possible obs: 99.7 % / Redundancy: 7.2 % / R_merge(I) obs: 1.251 / Num. measured all: 82295 / Num. unique obs: 11373 / CC_1/2: 0.742 / R_pim(I) all: 0.495 / R_rim(I) all: 1.346 / Χ²: 0.95 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	(dev_5438: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.15→49.03 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2297	7773	5.06 %
R_work	0.1928	-	-
obs	0.1947	153627	99.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.15→49.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20351	0	357	584	21292

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	21301
X-RAY DIFFRACTION	f_angle_d	0.763	29072
X-RAY DIFFRACTION	f_dihedral_angle_d	13.172	8037
X-RAY DIFFRACTION	f_chiral_restr	0.05	3461
X-RAY DIFFRACTION	f_plane_restr	0.008	3713

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 (%)
2.15-2.17	0.3314	276	0.2788	4870	X-RAY DIFFRACTION	100
2.17-2.2	0.3346	230	0.2732	4858	X-RAY DIFFRACTION	100
2.2-2.23	0.3435	227	0.2705	4847	X-RAY DIFFRACTION	100
2.23-2.26	0.325	254	0.2533	4825	X-RAY DIFFRACTION	99
2.26-2.28	0.3	251	0.2524	4865	X-RAY DIFFRACTION	100
2.28-2.32	0.2693	276	0.2373	4835	X-RAY DIFFRACTION	100
2.32-2.35	0.2757	280	0.2308	4820	X-RAY DIFFRACTION	100
2.35-2.38	0.2679	268	0.2264	4849	X-RAY DIFFRACTION	100
2.38-2.42	0.284	254	0.2336	4841	X-RAY DIFFRACTION	100
2.42-2.46	0.2635	263	0.2195	4856	X-RAY DIFFRACTION	100
2.46-2.5	0.265	246	0.2201	4831	X-RAY DIFFRACTION	100
2.5-2.55	0.2963	229	0.2123	4953	X-RAY DIFFRACTION	100
2.55-2.6	0.2617	250	0.211	4806	X-RAY DIFFRACTION	100
2.6-2.65	0.2524	226	0.2144	4895	X-RAY DIFFRACTION	100
2.65-2.71	0.2641	280	0.2158	4862	X-RAY DIFFRACTION	100
2.71-2.77	0.2898	280	0.2162	4807	X-RAY DIFFRACTION	100
2.77-2.84	0.2675	309	0.2264	4803	X-RAY DIFFRACTION	100
2.84-2.92	0.2964	251	0.2159	4918	X-RAY DIFFRACTION	100
2.92-3	0.261	244	0.2154	4861	X-RAY DIFFRACTION	100
3-3.1	0.2472	263	0.1979	4848	X-RAY DIFFRACTION	100
3.1-3.21	0.2288	234	0.1994	4894	X-RAY DIFFRACTION	100
3.21-3.34	0.2132	263	0.1932	4871	X-RAY DIFFRACTION	100
3.34-3.49	0.2271	289	0.198	4828	X-RAY DIFFRACTION	100
3.49-3.68	0.2308	270	0.1837	4857	X-RAY DIFFRACTION	100
3.68-3.91	0.1965	237	0.1665	4948	X-RAY DIFFRACTION	100
3.91-4.21	0.1842	272	0.1554	4862	X-RAY DIFFRACTION	100
4.21-4.63	0.1551	257	0.1358	4917	X-RAY DIFFRACTION	100
4.63-5.3	0.1693	246	0.1426	4865	X-RAY DIFFRACTION	99
5.3-6.67	0.1938	246	0.1648	4913	X-RAY DIFFRACTION	99
6.68-49.03	0.1838	302	0.1812	4849	X-RAY DIFFRACTION	98

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	0.6203	-0.0188	-0.1702	0.5157	0.2377	0.7067	-0.0177	-0.0466	-0.1148	0.0687	-0.0874	0.1099	0.1064	-0.0202	-0.0005	0.1906	-0.0003	0.0349	0.264	-0.0136	0.2762	-4.8773	-0.7044	27.018
2	0.6843	0.071	-0.2574	0.3001	-0.183	0.6627	-0.0504	0.0102	-0.1282	0.0264	-0.1092	-0.0714	0.1537	0.1507	-0.0069	0.2225	0.0358	0.0191	0.3184	0.0356	0.2616	34.8761	-0.525	32.6075
3	0.4342	0.2569	0.1163	0.6584	0.2527	0.4046	-0.0556	-0.0244	0.0537	0.1185	-0.0089	0.024	-0.032	-0.0876	-0.0001	0.2075	0.0282	-0.0251	0.2851	0.0021	0.182	11.002	28.426	48.1813
4	0.7485	-0.2107	-0.248	0.354	0.0877	0.5566	0.0547	-0.0071	0.1255	-0.0808	-0.0478	-0.0779	-0.1275	0.1199	0	0.207	-0.0074	-0.0096	0.2728	0.0082	0.2022	18.9941	26.7009	9.1142
5	0.2532	-0.0657	0.21	0.3167	-0.291	0.3742	0.0159	0.0042	-0.1169	-0.0524	-0.034	-0.0533	0.1088	0.0357	-0	0.251	-0.0037	0.0446	0.2271	0.0126	0.3529	44.4081	64.5481	45.402
6	0.4269	-0.048	0.1176	0.2614	0.287	0.4094	0.0274	-0.0878	-0.1116	-0.1538	-0.006	-0.0022	0.128	-0.0662	-0.0007	0.3303	-0.069	-0.0185	0.2605	0.0268	0.2658	5.0915	63.116	38.7649
7	0.8695	-0.0296	0.0916	0.4823	-0.1641	0.4613	-0.0398	0.0606	0.0302	-0.1349	-0.0213	-0.0755	0.0439	0.0862	-0	0.2512	-0.0339	0.0187	0.2445	-0.0089	0.2071	28.1607	92.1555	22.4984
8	0.6538	0.3086	-0.1165	0.5105	-0.1703	0.4755	-0.0176	-0.0714	-0.0189	0.0793	-0.0059	-0.0108	-0.0625	-0.0878	-0	0.1898	-0.0197	-0.0311	0.3193	0.0075	0.1961	18.9643	92.3869	61.1607

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H

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