PDB-9zag: Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase f...

ID or keywords:

Entry

Database: PDB / ID: 9zag

Title

Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD and GLYCERALDEHYDE-3-PHOSPHATE

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

Neisseria gonorrhoeae NCCP11945 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.91 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 a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD and GLYCERALDEHYDE-3-PHOSPHATE
Authors: Liu, L. / Lovell, S. / Seibold, S. / Battaile, K.P.

History

Deposition	Nov 19, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 3, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9zag.cif.gz	1009.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9zag.ent.gz	838.9 KB	Display	PDB format
PDBx/mmJSON format	9zag.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9zag_validation.pdf.gz	4.5 MB	Display	wwPDB validaton report
Full document	9zag_full_validation.pdf.gz	4.5 MB	Display
Data in XML	9zag_validation.xml.gz	127.8 KB	Display
Data in CIF	9zag_validation.cif.gz	161.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/za/9zag ftp://data.pdbj.org/pub/pdb/validation_reports/za/9zag	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 (10)

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

303 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
151 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.647, 105.543, 167.699
Angle α, β, γ (deg.)	90.00, 94.63, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	Glyceraldehyde-3-phosphate dehydrogenase Mass: 36829.789 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae NCCP11945 (bacteria) Gene: NGK_2321 / Plasmid: NegoA.00617.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B4RPP8, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor

#1: Protein

Glyceraldehyde-3-phosphate dehydrogenase

Mass: 36829.789 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Neisseria gonorrhoeae NCCP11945 (bacteria)
Gene: NGK_2321 / Plasmid: NegoA.00617.a.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B4RPP8, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 9 types, 1336 molecules

#2: Chemical	ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE Mass: 170.058 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₇O₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: 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
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#6: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#9: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1298 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.06 Å³/Da / Density % sol: 40.15 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Berkeley H9: 25% PEG 4000, 0.10M HEPES pH 7.5, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD and G3H, plate 20061 H9 drop 1, Puck: PSL-2203, Cryo: 80% ...Details: Berkeley H9: 25% PEG 4000, 0.10M HEPES pH 7.5, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD and G3H, plate 20061 H9 drop 1, Puck: PSL-2203, Cryo: 80% crystallant + 20% PEG 200

Crystal

Density Matthews: 2.06 Å³/Da / Density % sol: 40.15 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Berkeley H9: 25% PEG 4000, 0.10M HEPES pH 7.5, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD and G3H, plate 20061 H9 drop 1, Puck: PSL-2203, Cryo: 80% ...

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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: Jun 28, 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: 1.91→49.27 Å / Num. obs: 184320 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC_1/2: 0.996 / R_merge(I) obs: 0.178 / R_pim(I) all: 0.073 / R_rim(I) all: 0.192 / Χ²: 1.04 / Net I/σ(I): 9.8 / Num. measured all: 1270381
Reflection shell	Resolution: 1.91→1.96 Å / % possible obs: 100 % / Redundancy: 7.1 % / R_merge(I) obs: 1.309 / Num. measured all: 95836 / Num. unique obs: 13577 / CC_1/2: 0.581 / R_pim(I) all: 0.527 / R_rim(I) all: 1.413 / 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: 1.91→48.89 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.187	9113	4.95 %
R_work	0.1547	-	-
obs	0.1563	184233	99.9 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.91→48.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20011	0	549	1298	21858

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	20922
X-RAY DIFFRACTION	f_angle_d	1.031	28430
X-RAY DIFFRACTION	f_dihedral_angle_d	13.993	7991
X-RAY DIFFRACTION	f_chiral_restr	0.059	3336
X-RAY DIFFRACTION	f_plane_restr	0.012	3632

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 (%)
1.91-1.93	0.2954	283	0.2441	5764	X-RAY DIFFRACTION	100
1.93-1.95	0.2759	344	0.2279	5809	X-RAY DIFFRACTION	100
1.95-1.98	0.2615	293	0.217	5825	X-RAY DIFFRACTION	100
1.98-2	0.253	272	0.2106	5840	X-RAY DIFFRACTION	100
2-2.03	0.2494	303	0.2011	5869	X-RAY DIFFRACTION	100
2.03-2.06	0.2289	293	0.1893	5788	X-RAY DIFFRACTION	100
2.06-2.09	0.2193	318	0.1827	5828	X-RAY DIFFRACTION	100
2.09-2.12	0.231	301	0.1805	5826	X-RAY DIFFRACTION	100
2.12-2.15	0.2415	294	0.1841	5832	X-RAY DIFFRACTION	100
2.15-2.19	0.218	293	0.1652	5781	X-RAY DIFFRACTION	100
2.19-2.22	0.2049	302	0.1567	5864	X-RAY DIFFRACTION	100
2.22-2.26	0.2064	287	0.1524	5826	X-RAY DIFFRACTION	100
2.26-2.31	0.1908	264	0.1531	5880	X-RAY DIFFRACTION	100
2.31-2.36	0.2126	297	0.153	5849	X-RAY DIFFRACTION	100
2.36-2.41	0.2026	298	0.148	5811	X-RAY DIFFRACTION	100
2.41-2.46	0.1969	309	0.1472	5838	X-RAY DIFFRACTION	100
2.46-2.52	0.1987	295	0.1479	5853	X-RAY DIFFRACTION	100
2.52-2.59	0.2005	319	0.1458	5797	X-RAY DIFFRACTION	100
2.59-2.67	0.2084	324	0.1466	5838	X-RAY DIFFRACTION	100
2.67-2.75	0.1787	302	0.1384	5844	X-RAY DIFFRACTION	100
2.75-2.85	0.1789	298	0.1436	5871	X-RAY DIFFRACTION	100
2.85-2.97	0.206	312	0.156	5799	X-RAY DIFFRACTION	100
2.97-3.1	0.1962	295	0.1625	5872	X-RAY DIFFRACTION	100
3.1-3.27	0.1785	299	0.1535	5855	X-RAY DIFFRACTION	100
3.27-3.47	0.1774	315	0.1529	5820	X-RAY DIFFRACTION	100
3.47-3.74	0.1821	278	0.1467	5872	X-RAY DIFFRACTION	100
3.74-4.11	0.1646	301	0.1315	5868	X-RAY DIFFRACTION	100
4.11-4.71	0.1237	323	0.1153	5818	X-RAY DIFFRACTION	100
4.71-5.93	0.1425	336	0.1392	5889	X-RAY DIFFRACTION	100
5.93-48.89	0.1816	365	0.1753	5894	X-RAY DIFFRACTION	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	0.3156	0.1154	0.0496	0.3	0.0599	0.5973	-0.0227	-0.0496	-0.059	0.0567	0.006	-0.0578	0.1049	0.0734	-0	0.1533	0.0124	0.0004	0.1257	0.0223	0.164	16.8754	-27.3885	74.2835
2	0.2679	-0.0304	-0.0174	0.3061	0.0593	0.1972	-0.0054	-0.0353	0.0471	0.0445	-0.0346	0.0383	-0.0688	-0.0329	-0.0017	0.1806	0.0113	-0.0054	0.1309	-0.0222	0.1419	-5.068	4.1418	76.7791
3	0.4117	0.0026	-0.0849	0.3209	-0.114	0.3539	-0.045	0.0838	-0.0684	-0.0389	0.0182	0.056	-0.0062	-0.1225	-0.0061	0.1147	-0.0126	-0.0082	0.1639	-0.0294	0.1385	-15.0478	-21.0608	49.2477
4	0.4624	0.0529	-0.1047	0.3729	-0.0431	0.4381	-0.0264	0.0831	0.016	-0.0519	0.0076	-0.0809	-0.0562	0.0376	-0.0007	0.1535	-0.0062	0.0147	0.1539	0.017	0.1481	18.7487	-3.412	44.1784
5	0.3792	-0.1056	-0.354	0.3243	-0.0913	0.6682	-0.029	0.0859	-0.037	-0.0892	0.0036	0.0455	0.1066	-0.1774	-0.0036	0.1493	-0.0201	-0.0233	0.1823	0.0025	0.1402	10.4208	26.5243	7.6339
6	0.459	0.0093	-0.0085	0.3094	-0.0725	0.5304	0.0589	0.0824	0.1347	-0.0479	-0.0191	-0.0507	-0.1555	0.0475	0.0158	0.1933	-0.0041	0.0348	0.1249	0.0329	0.1942	32.6078	57.8622	8.5642
7	0.3405	-0.0355	-0.0584	0.4089	0.1025	0.4744	-0.003	-0.0627	0.0007	0.0417	0.0241	-0.1081	0.0366	0.1214	0.0001	0.1226	0.0061	-0.0193	0.1753	0.0057	0.1799	42.2036	30.285	33.5932
8	0.2376	0.0269	-0.0887	0.46	-0.0015	0.5748	0.0105	-0.0475	0.0416	0.0563	-0.008	0.0562	-0.0913	-0.0921	0.0001	0.1396	0.014	0.012	0.1618	-0.0083	0.1638	8.5751	47.5729	40.1919

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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