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- PDB-9fq4: Glyceraldehyde 3-phosphate dehydrogenase A (GAPDHA) NADP holoenzy... -

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Open data

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Basic information

Entry

Database: PDB / ID: 9fq4

Title

Glyceraldehyde 3-phosphate dehydrogenase A (GAPDHA) NADP holoenzyme, from Helicobacter pylori, with active site cysteine oxidised to sulfenic acid

Components

Glyceraldehyde-3-phosphate dehydrogenase (Gap)

Keywords

OXIDOREDUCTASE / holoenzyme / glyocolysis / gluconeogenesis / carbohydrate metabolism / Rossmann fold / Helicobacter pylori / nucleotide binding domain / B-nicotinamide adenine dinucleotide phosphate / NADP / sulfenic acid

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: 1.2 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 14, 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	9fq4.cif.gz	360 KB	Display	PDBx/mmCIF format
PDB format	pdb9fq4.ent.gz	221.8 KB	Display	PDB format
PDBx/mmJSON format	9fq4.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/fq/9fq4 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/9fq4	HTTPS FTP

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Related structure data

Related structure data	9fodC 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

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

Unit cell

Length a, b, c (Å)	85.478, 96.196, 94.728
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
2	1	A-774- HOH

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Components

#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: pET151/D / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: O25902
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H₂O
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: 54.39 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M NH4SO4, 0.1M Tris pH 8.5, 25% w/v PEG3350

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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: 1.2→38.362 Å / Num. obs: 120012 / % possible obs: 98.8 % / Redundancy: 23.9 % / CC_1/2: 1 / R_rim(I) all: 0.089 / Net I/σ(I): 22.2
Reflection shell	Resolution: 1.2→1.22 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5198 / CC_1/2: 0.896 / R_rim(I) all: 0.737 / % possible all: 87.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
xia2.multiplex		data reduction
xia2.multiplex		data scaling
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.2→38.362 Å / Cor.coef. F_o:F_c: 0.981 / Cor.coef. F_o:F_c free: 0.978 / WR_factor R_free: 0.138 / WR_factor R_work: 0.123 / SU B: 0.837 / SU ML: 0.017 / Average fsc free: 0.9894 / Average fsc work: 0.9923 / Cross valid method: FREE R-VALUE / ESU R: 0.027 / ESU R Free: 0.027
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1366	5943	4.952 %
R_work	0.1204	114065	-
all	0.121	-	-
obs	-	120008	98.745 %

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: 12.603 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.78 Å²	0 Å²	0 Å²
2-	-	0.307 Å²	0 Å²
3-	-	-	0.474 Å²

Refinement step

Cycle: LAST / Resolution: 1.2→38.362 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2534	0	53	312	2899

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	2687
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2596
X-RAY DIFFRACTION	r_angle_refined_deg	1.963	1.806	3665
X-RAY DIFFRACTION	r_angle_other_deg	0.707	1.761	5986
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.067	5	345
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.962	5	15
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.936	5	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.955	10	474
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.275	10	111
X-RAY DIFFRACTION	r_chiral_restr	0.137	0.2	443
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3108
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	579
X-RAY DIFFRACTION	r_nbd_refined	0.226	0.2	483
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	2317
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	1301
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	1505
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	188
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.21	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.148	0.2	120
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.194	0.2	39
X-RAY DIFFRACTION	r_mcbond_it	3.936	1.101	1341
X-RAY DIFFRACTION	r_mcbond_other	3.862	1.1	1341
X-RAY DIFFRACTION	r_mcangle_it	5.526	1.985	1681
X-RAY DIFFRACTION	r_mcangle_other	5.543	1.987	1682
X-RAY DIFFRACTION	r_scbond_it	6.814	1.405	1346
X-RAY DIFFRACTION	r_scbond_other	6.755	1.402	1340
X-RAY DIFFRACTION	r_scangle_it	9.487	2.427	1978
X-RAY DIFFRACTION	r_scangle_other	9.426	2.421	1973
X-RAY DIFFRACTION	r_lrange_it	14.45	14.064	2955
X-RAY DIFFRACTION	r_lrange_other	12.951	12.203	2881
X-RAY DIFFRACTION	r_rigid_bond_restr	4.647	3	5283

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.2-1.231	0.183	368	0.169	7564	0.17	8938	0.981	0.984	88.7447	0.146
1.231-1.265	0.15	392	0.139	7997	0.139	8682	0.987	0.989	96.6252	0.118
1.265-1.301	0.139	416	0.126	7927	0.127	8426	0.989	0.992	99.015	0.108
1.301-1.341	0.133	436	0.117	7724	0.118	8209	0.989	0.993	99.4031	0.099
1.341-1.385	0.131	413	0.109	7489	0.11	7935	0.99	0.994	99.5841	0.092
1.385-1.434	0.129	371	0.102	7349	0.103	7746	0.99	0.994	99.6643	0.087
1.434-1.488	0.122	389	0.096	7005	0.098	7411	0.991	0.995	99.7706	0.083
1.488-1.549	0.116	333	0.094	6831	0.095	7171	0.992	0.995	99.9024	0.082
1.549-1.617	0.11	315	0.091	6550	0.092	6869	0.992	0.995	99.9418	0.081
1.617-1.696	0.122	318	0.095	6299	0.097	6617	0.99	0.995	100	0.086
1.696-1.788	0.122	312	0.091	5959	0.093	6271	0.991	0.995	100	0.084
1.788-1.896	0.116	330	0.101	5617	0.102	5947	0.992	0.994	100	0.096
1.896-2.027	0.113	291	0.11	5279	0.11	5570	0.992	0.994	100	0.107
2.027-2.188	0.123	262	0.111	4958	0.112	5220	0.992	0.993	100	0.112
2.188-2.396	0.148	220	0.112	4594	0.114	4814	0.987	0.993	100	0.116
2.396-2.678	0.13	201	0.124	4186	0.124	4387	0.99	0.99	100	0.131
2.678-3.09	0.163	184	0.134	3691	0.135	3875	0.985	0.989	100	0.147
3.09-3.778	0.14	162	0.132	3140	0.132	3302	0.989	0.989	100	0.151
3.778-5.317	0.153	151	0.139	2463	0.139	2614	0.99	0.991	100	0.167
5.317-38.362	0.192	79	0.211	1443	0.21	1523	0.984	0.98	99.9343	0.295

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