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

ID or keywords:

Entry

Database: PDB / ID: 9pgq

Title

Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase from Bordetella pertussis (Apo, trigonal form)

Components

Glyceraldehyde-3-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Bordetella pertussis / 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: 1.5 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 (Apo, trigonal form)
Authors: Ung, A.R. / Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Jul 8, 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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Download

PDBx/mmCIF format	9pgq.cif.gz	277.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9pgq.ent.gz	222.5 KB	Display	PDB format
PDBx/mmJSON format	9pgq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9pgq_validation.pdf.gz	471.1 KB	Display	wwPDB validaton report
Full document	9pgq_full_validation.pdf.gz	476 KB	Display
Data in XML	9pgq_validation.xml.gz	35.8 KB	Display
Data in CIF	9pgq_validation.cif.gz	49.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pg/9pgq ftp://data.pdbj.org/pub/pdb/validation_reports/pg/9pgq	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

hetero molecules

75.5 kDa, 2 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

A: Glyceraldehyde-3-phosphate dehydrogenase

B: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.461, 83.461, 166.173
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-552- HOH
2	1	A-734- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Glyceraldehyde-3-phosphate dehydrogenase Mass: 37360.496 Da / Num. of mol.: 2 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

#1: Protein

Glyceraldehyde-3-phosphate dehydrogenase

Mass: 37360.496 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 482 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 2.24 Å³/Da / Density % sol: 44.99 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Index H1: 100 mM Tris, pH 8.5, 200 mM MgCl2, 25% (w/v) PEG 3350. BopeA.00052.a.B2.PW39379 at 12.4 mg/mL. 5mM NAD and D-glyceraldehyde-3-phosphate added to the protein prior to ...Details: Index H1: 100 mM Tris, pH 8.5, 200 mM MgCl2, 25% (w/v) PEG 3350. BopeA.00052.a.B2.PW39379 at 12.4 mg/mL. 5mM NAD and D-glyceraldehyde-3-phosphate added to the protein prior to crystallization but no electron density for the ligands was observed. plate 19840 well H1 drop 3 , Puck: PSL-2105, Cryo: 80% crystallant + 20% PEG 200

Crystal

Density Matthews: 2.24 Å³/Da / Density % sol: 44.99 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Index H1: 100 mM Tris, pH 8.5, 200 mM MgCl2, 25% (w/v) PEG 3350. BopeA.00052.a.B2.PW39379 at 12.4 mg/mL. 5mM NAD and D-glyceraldehyde-3-phosphate added to the protein prior to ...

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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: 1.5→43.97 Å / Num. obs: 107896 / % possible obs: 100 % / Redundancy: 20.2 % / CC_1/2: 1 / R_merge(I) obs: 0.108 / R_pim(I) all: 0.025 / R_rim(I) all: 0.111 / Χ²: 1 / Net I/σ(I): 17.7 / Num. measured all: 2177860
Reflection shell	Resolution: 1.5→1.53 Å / % possible obs: 100 % / Redundancy: 20.9 % / R_merge(I) obs: 2.386 / Num. measured all: 109904 / Num. unique obs: 5248 / CC_1/2: 0.376 / R_pim(I) all: 0.533 / R_rim(I) all: 2.445 / Χ²: 0.98 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	(2.0_5750: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→43.97 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1856	5393	5 %
R_work	0.1625	-	-
obs	0.1636	107818	99.99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.5→43.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5044	0	52	474	5570

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5248
X-RAY DIFFRACTION	f_angle_d	1.057	7157
X-RAY DIFFRACTION	f_dihedral_angle_d	15.105	1895
X-RAY DIFFRACTION	f_chiral_restr	0.062	861
X-RAY DIFFRACTION	f_plane_restr	0.011	918

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 (%)
1.5-1.52	0.299	174	0.3168	3378	X-RAY DIFFRACTION	100
1.52-1.53	0.3128	173	0.2956	3376	X-RAY DIFFRACTION	100
1.53-1.55	0.3136	207	0.2826	3317	X-RAY DIFFRACTION	100
1.55-1.57	0.2487	168	0.2656	3429	X-RAY DIFFRACTION	100
1.57-1.59	0.2869	187	0.2569	3312	X-RAY DIFFRACTION	100
1.59-1.62	0.2856	210	0.2439	3356	X-RAY DIFFRACTION	100
1.62-1.64	0.2611	177	0.2371	3381	X-RAY DIFFRACTION	100
1.64-1.66	0.2488	163	0.2233	3413	X-RAY DIFFRACTION	100
1.66-1.69	0.2687	215	0.2071	3320	X-RAY DIFFRACTION	100
1.69-1.72	0.219	160	0.2007	3408	X-RAY DIFFRACTION	100
1.72-1.75	0.2359	157	0.1961	3411	X-RAY DIFFRACTION	100
1.75-1.78	0.2149	206	0.1906	3368	X-RAY DIFFRACTION	100
1.78-1.81	0.2021	164	0.1849	3418	X-RAY DIFFRACTION	100
1.81-1.85	0.2026	175	0.1772	3367	X-RAY DIFFRACTION	100
1.85-1.89	0.2033	185	0.1754	3384	X-RAY DIFFRACTION	100
1.89-1.93	0.1988	191	0.1667	3406	X-RAY DIFFRACTION	100
1.93-1.98	0.2004	197	0.1554	3377	X-RAY DIFFRACTION	100
1.98-2.04	0.1944	172	0.1515	3411	X-RAY DIFFRACTION	100
2.04-2.1	0.1657	153	0.1484	3434	X-RAY DIFFRACTION	100
2.1-2.16	0.1701	199	0.1468	3370	X-RAY DIFFRACTION	100
2.16-2.24	0.1742	177	0.1404	3418	X-RAY DIFFRACTION	100
2.24-2.33	0.1493	161	0.1429	3437	X-RAY DIFFRACTION	100
2.33-2.44	0.1786	183	0.1427	3412	X-RAY DIFFRACTION	100
2.44-2.56	0.176	191	0.146	3424	X-RAY DIFFRACTION	100
2.56-2.73	0.1741	168	0.1513	3440	X-RAY DIFFRACTION	100
2.73-2.94	0.1872	183	0.1556	3461	X-RAY DIFFRACTION	100
2.94-3.23	0.1826	182	0.1573	3453	X-RAY DIFFRACTION	100
3.23-3.7	0.17	181	0.1524	3493	X-RAY DIFFRACTION	100
3.7-4.66	0.1463	184	0.1295	3528	X-RAY DIFFRACTION	100
4.66-43.97	0.1718	150	0.1651	3723	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	2.31	-0.0125	-0.1241	1.7712	0.338	1.5317	0.0234	0.2864	-0.2849	-0.1431	-0.0772	-0.0464	0.1523	-0.0184	0.0465	0.1218	0.0069	0.0274	0.1924	-0.0183	0.1475	4.1007	23.9929	11.3925
2	0.6815	-0.1338	-0.1621	0.609	-0.0214	0.4956	0.0537	0.0245	0.0624	0.0708	-0.0267	-0.1272	-0.0834	0.0927	-0.0344	0.1288	-0.0176	-0.012	0.138	0.0054	0.1406	2.5915	41.853	27.3191
3	0.2247	-0.3616	-0.3253	0.6681	0.5967	0.5335	0.2992	-0.0136	0.6283	0.3636	-0.0253	0.8194	-0.2596	-0.2423	0.0367	0.5533	-0.0108	0.3443	0.3097	-0.0098	0.7286	-38.5334	49.1267	48.7778
4	0.2468	-0.396	0.0767	0.8786	-0.1555	0.0333	0.0678	-0.1767	0.4633	0.3378	-0.0518	0.4984	-0.3125	-0.1532	0.1041	0.7889	-0.021	0.5078	0.0246	-0.2207	0.8046	-26.2346	62.6387	52.3364
5	1.7598	0.3002	0.1743	0.892	0.0918	1.5132	0.0763	-0.1667	0.1451	0.4668	-0.0783	0.0148	-0.0461	0.0901	0.0072	0.363	-0.0687	0.0212	0.1467	-0.0193	0.1706	-6.1593	50.8978	48.6635
6	0.628	0.2535	-0.5926	3.3849	-1.0819	1.965	0.1544	-0.0194	0.7465	0.268	0.039	0.3056	-0.556	-0.1216	-0.1749	0.2509	0.0153	0.0588	0.1799	0.0265	0.4114	-21.0683	51.7771	26.0441
7	0.9201	0.806	1.1955	2.0802	2.2888	3.6341	0.0714	-0.1644	0.2214	0.3515	-0.163	0.3146	-0.2072	-0.1323	0.1093	0.3627	-0.0542	0.0917	0.1512	-0.0154	0.2297	-10.026	55.0834	41.0044
8	1.4907	0.3304	0.1306	1.465	0.003	0.8518	-0.0327	-0.0712	0.1769	0.2166	0.0083	-0.0607	-0.1463	0.0808	0.0397	0.2372	-0.0427	0.0121	0.1191	-0.0164	0.1595	-5.5868	47.5098	42.3799
9	0.8702	0.1234	0.9689	1.0569	0.9439	1.7192	0.1642	-0.3024	-0.0894	0.6889	-0.0721	-0.0146	0.0133	-0.06	-0.0448	0.5254	-0.0925	-0.0279	0.2342	0.0149	0.1568	-7.0495	39.2946	55.7582
10	0.9611	-0.3003	0.549	0.8947	0.3295	0.7459	0.2452	-0.107	0.3217	0.5237	-0.1795	0.1759	-0.0942	-0.0806	-0.0183	0.3959	-0.0835	0.1041	0.1496	-0.018	0.2322	-14.9729	45.0019	49.8653

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 142 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 143 through 336 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 2 through 88 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 89 through 154 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 155 through 183 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 184 through 203 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 204 through 229 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 230 through 256 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 257 through 284 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 285 through 336 )

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