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- PDB-7bex: Glyceraldehyde 3-phosphate dehydrogenase from Campylobacter jejeu... -

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Open data

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Basic information

Entry

Database: PDB / ID: 7bex

Title

Glyceraldehyde 3-phosphate dehydrogenase from Campylobacter jejeuni - ADP complex

Components

Glyceraldehyde-3-phosphate dehydrogenase

Glyceraldehyde 3-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE / Dehydrogenase Nucleoside binding Glycolysis Gluconeogenesis

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

Campylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.054 Å

Authors

Moody, P.C.E. / Ayna, A.

Citation

Journal: To Be Published
Title: structure of Camplylobacter jejueni GAPDH in complex with ADP
Authors: Moody, P.C.E. / Ayna, A.

History

Deposition	Dec 29, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 12, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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	7bex.cif.gz	88.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7bex.ent.gz	62.3 KB	Display	PDB format
PDBx/mmJSON format	7bex.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/be/7bex ftp://data.pdbj.org/pub/pdb/validation_reports/be/7bex	HTTPS FTP

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Related structure data

Related structure data	7bewS S: Starting model for refinement
Similar structure data	3rvd-3 2pkr-2 3cmc-d 4lsm-2 4p8r-d 1jn0-1 3rvd-2 3rvd-1 1jn0-2 2d2i-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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) #234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1)

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Assembly

Deposited unit

A: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

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

1

A: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	90.250, 90.250, 223.390
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	98
Space group name H-M	I4₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-573- HOH
2	1	A-686- HOH
3	1	A-699- HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein

Glyceraldehyde-3-phosphate dehydrogenase /

Glyceraldehyde 3-phosphate dehydrogenase

Mass: 36418.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: gapA, Cj1403c / Plasmid: pCJgapA / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q0P8L1,

Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 5 types, 217 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS
#5: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 3.16 Å³/Da / Density % sol: 61.03 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1M Sodium Acetate, 2.0 M Ammonium Sulfate,

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU / Detector: CCD / Date: Apr 1, 2013 / Details: varimax HF
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.05→83.67 Å / Num. obs: 29280 / % possible obs: 91.3 % / Redundancy: 10.9 % / R_merge(I) obs: 0.13 / Net I/σ(I): 9.9
Reflection shell	Resolution: 2.05→2.11 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.32 / Num. unique obs: 2225 / % possible all: 94.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
iMOSFLM		data reduction
pointless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7BEW

Resolution: 2.054→30.105 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.935 / SU B: 3.049 / SU ML: 0.083 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.127
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1905	1437	4.912 %	random
R_work	0.1546	27815	-	-
all	0.156	-	-	-
obs	-	29252	99.898 %	-

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: 17.297 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.007 Å²	0 Å²	-0 Å²
2-	-	-0.007 Å²	0 Å²
3-	-	-	0.014 Å²

Refinement step

Cycle: LAST / Resolution: 2.054→30.105 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2519	0	49	211	2779

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	2641
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2547
X-RAY DIFFRACTION	r_angle_refined_deg	1.709	1.635	3578
X-RAY DIFFRACTION	r_angle_other_deg	1.422	1.589	5871
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.513	5	340
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.285	23.28	125
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.756	15	476
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.219	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	365
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2984
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	567
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	487
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	2367
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	1254
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	1314
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	177
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.163	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.187	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.144	0.2	85
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.198	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	1.619	1.579	1331
X-RAY DIFFRACTION	r_mcbond_other	1.607	1.577	1329
X-RAY DIFFRACTION	r_mcangle_it	2.493	2.358	1665
X-RAY DIFFRACTION	r_mcangle_other	2.494	2.359	1666
X-RAY DIFFRACTION	r_scbond_it	2.981	1.926	1310
X-RAY DIFFRACTION	r_scbond_other	2.98	1.926	1311
X-RAY DIFFRACTION	r_scangle_it	4.376	2.748	1908
X-RAY DIFFRACTION	r_scangle_other	4.375	2.748	1909
X-RAY DIFFRACTION	r_lrange_it	5.817	19.295	2877
X-RAY DIFFRACTION	r_lrange_other	5.774	19.107	2851

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 (%)
2.054-2.108	0.187	106	0.175	2025	X-RAY DIFFRACTION	99.6726
2.108-2.165	0.222	101	0.165	1954	X-RAY DIFFRACTION	100
2.165-2.228	0.222	99	0.16	1917	X-RAY DIFFRACTION	99.9009
2.228-2.297	0.204	102	0.149	1873	X-RAY DIFFRACTION	100
2.297-2.372	0.17	83	0.144	1815	X-RAY DIFFRACTION	100
2.372-2.455	0.205	99	0.151	1748	X-RAY DIFFRACTION	100
2.455-2.548	0.201	77	0.146	1698	X-RAY DIFFRACTION	100
2.548-2.651	0.19	87	0.15	1632	X-RAY DIFFRACTION	100
2.651-2.769	0.188	87	0.151	1562	X-RAY DIFFRACTION	100
2.769-2.904	0.234	69	0.158	1517	X-RAY DIFFRACTION	100
2.904-3.061	0.171	76	0.162	1428	X-RAY DIFFRACTION	100
3.061-3.247	0.201	76	0.155	1362	X-RAY DIFFRACTION	100
3.247-3.47	0.176	62	0.146	1296	X-RAY DIFFRACTION	100
3.47-3.748	0.146	69	0.14	1188	X-RAY DIFFRACTION	100
3.748-4.105	0.181	57	0.14	1119	X-RAY DIFFRACTION	100
4.105-4.588	0.143	52	0.132	1005	X-RAY DIFFRACTION	99.8111
4.588-5.295	0.144	46	0.141	912	X-RAY DIFFRACTION	100
5.295-6.478	0.349	38	0.201	778	X-RAY DIFFRACTION	99.8776
6.478-9.135	0.197	30	0.183	624	X-RAY DIFFRACTION	100
9.135-30.105	0.261	21	0.24	362	X-RAY DIFFRACTION	95.5112

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