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- PDB-9fod: Glyceraldehyde 3-phosphate dehydrogenase A (GAPDHA) apoenzyme, fr... -

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Open data

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Basic information

Entry

Database: PDB / ID: 9fod

Title

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

Components

Glyceraldehyde-3-phosphate dehydrogenase (Gap)

Keywords

OXIDOREDUCTASE / apoenzyme / glyocolysis / gluconeogenesis / carbohydrate metabolism / Rossmann fold / Helicobacter pylori / nucleotide binding domain

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: 1.444 Å

Authors

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

Funding support

United Kingdom, 1items

Citation

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

History

Deposition	Jun 11, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 25, 2025	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	9fod.cif.gz	343.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9fod.ent.gz	213.6 KB	Display	PDB format
PDBx/mmJSON format	9fod.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9fod_validation.pdf.gz	435.6 KB	Display	wwPDB validaton report
Full document	9fod_full_validation.pdf.gz	437.4 KB	Display
Data in XML	9fod_validation.xml.gz	18.8 KB	Display
Data in CIF	9fod_validation.cif.gz	26.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fo/9fod ftp://data.pdbj.org/pub/pdb/validation_reports/fo/9fod	HTTPS FTP

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Related structure data

Related structure data	9fq4C 9fl1 9fob C: citing same article (ref.)
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)

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Assembly

Deposited unit

A: Glyceraldehyde-3-phosphate dehydrogenase (Gap)

hetero molecules

36.3 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
Evidence: Crystallographic symmetry mates provides biological assembly (222 symmetry)
145 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.938, 94.811, 95.726
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-511- HOH

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Components

#1: Protein	Glyceraldehyde-3-phosphate dehydrogenase (Gap) Mass: 36069.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: HP_1346 / Plasmid: pET151/D / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: O25902
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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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: 2.82 Å³/Da / Density % sol: 56.38 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M NH4SO4, 0.1M Bis-Tris pH 6.5, 25% w/v PEG3350 300nl drop, mixed either 1:1 or 2:1

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 2, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.44→67.36 Å / Num. obs: 55539 / % possible obs: 95.4 % / Redundancy: 13.7 % / CC_1/2: 0.999 / R_rim(I) all: 0.088 / Net I/σ(I): 16.6
Reflection shell	Resolution: 1.44→1.57 Å / Redundancy: 13.7 % / Num. unique obs: 2777 / CC_1/2: 0.741 / R_rim(I) all: 1.838 / % possible all: 69.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
autoPROC		data reduction
STARANISO		data scaling
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.444→67.36 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.956 / SU B: 3.011 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1767	2795	5.032 %
R_work	0.1403	52744	-
all	0.142	-	-
obs	-	55539	77.25 %

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: 18.895 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.609 Å²	0 Å²	-0 Å²
2-	-	3.276 Å²	0 Å²
3-	-	-	-0.667 Å²

Refinement step

Cycle: LAST / Resolution: 1.444→67.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2476	0	10	269	2755

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	2549
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2482
X-RAY DIFFRACTION	r_angle_refined_deg	1.769	1.637	3463
X-RAY DIFFRACTION	r_angle_other_deg	0.624	1.578	5720
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.99	5	331
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.601	5	13
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.302	10	454
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.106	10	106
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	418
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2954
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	546
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	448
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.206	0.2	2148
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	1249
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	1384
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.184	0.2	157
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.148	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.152	0.2	76
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.122	0.2	37
X-RAY DIFFRACTION	r_mcbond_it	1.483	1.708	1300
X-RAY DIFFRACTION	r_mcbond_other	1.475	1.707	1300
X-RAY DIFFRACTION	r_mcangle_it	2.101	3.072	1624
X-RAY DIFFRACTION	r_mcangle_other	2.101	3.074	1625
X-RAY DIFFRACTION	r_scbond_it	2.14	2.218	1249
X-RAY DIFFRACTION	r_scbond_other	2.109	2.209	1242
X-RAY DIFFRACTION	r_scangle_it	2.936	3.855	1834
X-RAY DIFFRACTION	r_scangle_other	2.874	3.833	1823
X-RAY DIFFRACTION	r_lrange_it	3.782	19.413	2762
X-RAY DIFFRACTION	r_lrange_other	3.587	17.819	2708
X-RAY DIFFRACTION	r_rigid_bond_restr	5.652	3	5031

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 (%)
1.444-1.481	0.218	11	0.307	303	X-RAY DIFFRACTION	5.973
1.481-1.522	0.269	26	0.288	852	X-RAY DIFFRACTION	17.1083
1.522-1.566	0.282	104	0.239	1503	X-RAY DIFFRACTION	32.1529
1.566-1.614	0.262	138	0.223	2476	X-RAY DIFFRACTION	54.1762
1.614-1.667	0.245	201	0.214	3389	X-RAY DIFFRACTION	75.9788
1.667-1.726	0.239	179	0.196	3951	X-RAY DIFFRACTION	91.0695
1.726-1.791	0.191	199	0.156	4215	X-RAY DIFFRACTION	99.9547
1.791-1.864	0.179	225	0.13	4010	X-RAY DIFFRACTION	100
1.864-1.947	0.178	225	0.116	3830	X-RAY DIFFRACTION	100
1.947-2.041	0.15	188	0.115	3713	X-RAY DIFFRACTION	100
2.041-2.152	0.162	196	0.118	3515	X-RAY DIFFRACTION	100
2.152-2.282	0.171	178	0.122	3346	X-RAY DIFFRACTION	100
2.282-2.44	0.17	127	0.121	3193	X-RAY DIFFRACTION	100
2.44-2.635	0.154	171	0.121	2899	X-RAY DIFFRACTION	100
2.635-2.886	0.164	191	0.125	2668	X-RAY DIFFRACTION	100
2.886-3.226	0.158	119	0.127	2488	X-RAY DIFFRACTION	100
3.226-3.723	0.134	126	0.125	2158	X-RAY DIFFRACTION	100
3.723-4.556	0.151	87	0.125	1874	X-RAY DIFFRACTION	100
4.556-6.429	0.24	46	0.197	1505	X-RAY DIFFRACTION	100
6.429-67.36	0.291	58	0.226	855	X-RAY DIFFRACTION	100

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