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- PDB-9i5f: Glyceraldehyde 3-phosphate dehydrogenase A (GAPDHA) NAD holoenzym... -

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Open data

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Basic information

Entry

Database: PDB / ID: 9i5f

Title

Glyceraldehyde 3-phosphate dehydrogenase A (GAPDHA) NAD holoenzyme, from Helicobacter pylori

Components

Glyceraldehyde-3-phosphate dehydrogenase (Gap)

Keywords

OXIDOREDUCTASE / Holoenzyme / glycolysis / gluconeogenesis / carbohydrate metabolism / Rossmann fold / Helicobacter pylori / nucleotide binding domain / nicotinamide adenine dinucleotide

Function / homology

Function and homology information

glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / NADP binding / cytosol
Similarity search - Function

Biological species

Helicobacter pylori 26695 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.162 Å

Authors

Foster, S.P. / Moody, P.C.E.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Glyceraldehyde 3-phosphate dehydrogenae A (GAPDHA) NAD holoenzyme, from Helicobacter pylori
Authors: Foster, S.P. / Moody, P.C.E.

History

Deposition	Jan 28, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 18, 2026	Provider: repository / Type: Initial release

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	9i5f.cif.gz	370.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9i5f.ent.gz	228.8 KB	Display	PDB format
PDBx/mmJSON format	9i5f.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/i5/9i5f ftp://data.pdbj.org/pub/pdb/validation_reports/i5/9i5f	HTTPS FTP

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Related structure data

Related structure data	9fod 9fq4
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 (7) #13 - Jan 2001 Alcohol Dehydrogenase similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

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Assembly

Deposited unit

A: Glyceraldehyde-3-phosphate dehydrogenase (Gap)

hetero molecules

37.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glyceraldehyde-3-phosphate dehydrogenase (Gap)

hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase (Gap)

hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase (Gap)

hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase (Gap)

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.936, 94.866, 95.701
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-525- HOH
2	1	A-777- HOH
3	1	A-799- HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein

Glyceraldehyde-3-phosphate dehydrogenase (Gap)

Mass: 36101.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Helicobacter pylori 26695 (bacteria) / Gene: HP_1346 / Plasmid: pETE151/D / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: O25902

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Non-polymers , 6 types, 327 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EOH / ETHANOL Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O
#4: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Chemical	ChemComp-ART / ARSENATE Mass: 138.919 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AsO₄ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54.47 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 200mM sodium citrate tribasic 20% PEG 3350 (w/v) solution was mixed 4:1:1 or 3:2:1 (protein: reservoir: seeds) in 300nl drops.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.6888 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 24, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.6888 Å / Relative weight: 1
Reflection	Resolution: 1.16→67.37 Å / Num. obs: 82091 / % possible obs: 94.1 % / Redundancy: 13.8 % / CC_1/2: 0.997 / R_rim(I) all: 0.13 / Net I/σ(I): 11.3
Reflection shell	Resolution: 1.16→1.31 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4105 / CC_1/2: 0.833 / R_rim(I) all: 1.703 / % possible all: 62.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
autoPROC		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.162→67.37 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.971 / SU B: 1.95 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.045
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1637	4194	5.109 %
R_work	0.1364	77895	-
all	0.138	-	-
obs	-	82089	61.302 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 13.238 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.003 Å²	-0 Å²	0 Å²
2-	-	2.154 Å²	-0 Å²
3-	-	-	-0.151 Å²

Refinement step

Cycle: LAST / Resolution: 1.162→67.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2534	0	70	318	2922

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	2766
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	2678
X-RAY DIFFRACTION	r_angle_refined_deg	1.989	1.808	3787
X-RAY DIFFRACTION	r_angle_other_deg	0.843	1.763	6191
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.122	5	362
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.62	5	15
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.071	5	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.376	10	494
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.602	10	113
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	462
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	3193
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	590
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	495
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	2459
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	1299
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1529
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	205
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.127	0.2	34
X-RAY DIFFRACTION	r_nbd_other	0.15	0.2	190
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.13	0.2	52
X-RAY DIFFRACTION	r_mcbond_it	3.557	1.183	1364
X-RAY DIFFRACTION	r_mcbond_other	3.52	1.183	1364
X-RAY DIFFRACTION	r_mcangle_it	5.195	2.135	1716
X-RAY DIFFRACTION	r_mcangle_other	5.202	2.137	1717
X-RAY DIFFRACTION	r_scbond_it	5.946	1.465	1402
X-RAY DIFFRACTION	r_scbond_other	5.727	1.453	1391
X-RAY DIFFRACTION	r_scangle_it	8.327	2.574	2056
X-RAY DIFFRACTION	r_scangle_other	8.178	2.546	2039
X-RAY DIFFRACTION	r_lrange_it	15.107	15.655	3044
X-RAY DIFFRACTION	r_lrange_other	13.858	13.384	2977
X-RAY DIFFRACTION	r_rigid_bond_restr	4.95	3	5444

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 (%)
1.162-1.192	0.309	27	0.227	390	X-RAY DIFFRACTION	4.2258
1.192-1.225	0.211	30	0.224	630	X-RAY DIFFRACTION	6.9444
1.225-1.26	0.269	44	0.224	979	X-RAY DIFFRACTION	10.9611
1.26-1.299	0.273	96	0.232	1485	X-RAY DIFFRACTION	17.4542
1.299-1.342	0.23	148	0.216	2446	X-RAY DIFFRACTION	29.6017
1.342-1.389	0.218	202	0.209	3754	X-RAY DIFFRACTION	46.4756
1.389-1.441	0.239	269	0.197	4915	X-RAY DIFFRACTION	63.3896
1.441-1.5	0.207	308	0.18	5483	X-RAY DIFFRACTION	73.1095
1.5-1.567	0.177	313	0.157	6108	X-RAY DIFFRACTION	84.2762
1.567-1.643	0.173	322	0.143	6308	X-RAY DIFFRACTION	91.7647
1.643-1.732	0.173	356	0.132	6506	X-RAY DIFFRACTION	99.0331
1.732-1.837	0.152	313	0.123	6233	X-RAY DIFFRACTION	100
1.837-1.964	0.143	317	0.122	5841	X-RAY DIFFRACTION	99.9838
1.964-2.121	0.151	309	0.117	5406	X-RAY DIFFRACTION	99.4951
2.121-2.323	0.139	279	0.109	5046	X-RAY DIFFRACTION	100
2.323-2.597	0.155	253	0.114	4551	X-RAY DIFFRACTION	100
2.597-2.998	0.163	238	0.126	4037	X-RAY DIFFRACTION	100
2.998-3.67	0.187	157	0.129	3473	X-RAY DIFFRACTION	100
3.67-5.182	0.127	158	0.127	2698	X-RAY DIFFRACTION	100
5.182-67.37	0.213	55	0.206	1606	X-RAY DIFFRACTION	100

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