PDB-8jb1: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase fro...

ID or keywords:

Entry

Database: PDB / ID: 8jb1

Title

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum ATCC13032 in complex with NADP

Components

Glyceraldehyde-3-phosphate dehydrogenase

Keywords

STRUCTURAL PROTEIN / glycolysis / dehydrogenase

Function / homology

NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :

Function and homology information

Biological species

Corynebacterium glutamicum ATCC 13032 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.44 Å

Authors

Son, H.F. / Kim, K.J.

Funding support

Korea, Republic Of, 1items

Citation

Journal: Int.J.Biol.Macromol. / Year: 2023
Title: Structure-based functional analysis of a novel NADPH-producing glyceraldehyde-3-phosphate dehydrogenase from Corynebacterium glutamicum.
Authors: Son, H.F. / Park, W. / Kim, S. / Kim, I.K. / Kim, K.J.

History

Deposition	May 7, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 6, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8jb1.cif.gz	197.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8jb1.ent.gz	157 KB	Display	PDB format
PDBx/mmJSON format	8jb1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8jb1_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8jb1_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8jb1_validation.xml.gz	36.6 KB	Display
Data in CIF	8jb1_validation.cif.gz	50.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jb/8jb1 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/8jb1	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glyceraldehyde-3-phosphate dehydrogenase

B: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

110 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glyceraldehyde-3-phosphate dehydrogenase

B: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase

B: Glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	92.754, 92.754, 287.554
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	95
Space group name H-M	P4₃22

#1: Protein	Glyceraldehyde-3-phosphate dehydrogenase Mass: 54341.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria) Gene: gapX / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8G0FZM1
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.85 Å³/Da / Density % sol: 56.77 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG 3K, HEPES/NaOH, sodium chloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å

Detector

Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 29, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.987 Å / Relative weight: 1

Reflection

Resolution: 2.44→50 Å / Num. obs: 45137 / % possible obs: 94.7 % / Redundancy: 8.3 % / CC_1/2: 0.795 / Net I/σ(I): 13.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.45-2.49	4.9	0.295	2089	0.795	0.941	0.133	0.326	1.303	90.9
2.49-2.54	5	0.285	2154	0.823	0.95	0.128	0.314	1.41	91.6
2.54-2.59	4.9	0.276	2119	0.875	0.966	0.124	0.305	1.455	91.3
2.59-2.64	5.3	0.262	2145	0.861	0.962	0.115	0.288	1.437	91.9
2.64-2.7	5.6	0.249	2157	0.872	0.965	0.105	0.272	1.466	92.3
2.7-2.76	5.6	0.235	2161	0.921	0.979	0.098	0.256	1.599	92.7
2.76-2.83	6.2	0.209	2206	0.942	0.985	0.083	0.226	1.665	93.6
2.83-2.9	6.7	0.192	2234	0.959	0.989	0.073	0.206	1.765	94
2.9-2.99	7.3	0.169	2203	0.979	0.995	0.061	0.18	1.908	94.8
2.99-3.09	7.7	0.16	2214	0.984	0.996	0.056	0.17	2.003	94.5
3.09-3.2	8	0.145	2253	0.986	0.997	0.05	0.154	2.191	94.8
3.2-3.32	8.8	0.124	2270	0.992	0.998	0.04	0.131	2.344	95.8
3.32-3.48	9.7	0.109	2268	0.996	0.999	0.034	0.115	2.712	96.2
3.48-3.66	10.3	0.099	2294	0.996	0.999	0.03	0.103	2.919	96.7
3.66-3.89	10.7	0.09	2308	0.996	0.999	0.027	0.094	3.194	96.7
3.89-4.19	11.2	0.081	2338	0.997	0.999	0.024	0.085	3.559	97.6
4.19-4.61	11.9	0.075	2374	0.997	0.999	0.021	0.078	3.832	97.9
4.61-5.28	11.7	0.069	2385	0.998	0.999	0.02	0.072	3.57	97.6
5.28-6.65	11.3	0.068	2422	0.998	0.999	0.02	0.071	3.235	97.6
6.65-50	10.3	0.062	2543	0.997	0.999	0.019	0.065	3.69	95

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.44→31.54 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.902 / SU B: 9.538 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26249	2189	4.8 %	RANDOM
R_work	0.19246	-	-	-
obs	0.19589	42947	94.81 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 44.059 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.9 Å²	-0 Å²	-0 Å²
2-	-	0.9 Å²	-0 Å²
3-	-	-	-1.8 Å²

Refinement step

Cycle: 1 / Resolution: 2.44→31.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7292	0	114	130	7536

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	7532
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7179
X-RAY DIFFRACTION	r_angle_refined_deg	1.608	1.647	10254
X-RAY DIFFRACTION	r_angle_other_deg	0.53	1.576	16422
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.153	5	932
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.168	5	71
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.161	10	1240
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	1206
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	8941
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1749
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	4.291	4.337	3740
X-RAY DIFFRACTION	r_mcbond_other	4.289	4.337	3740
X-RAY DIFFRACTION	r_mcangle_it	6.575	7.778	4668
X-RAY DIFFRACTION	r_mcangle_other	6.574	7.779	4669
X-RAY DIFFRACTION	r_scbond_it	4.589	4.707	3792
X-RAY DIFFRACTION	r_scbond_other	4.589	4.707	3793
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.269	8.444	5587
X-RAY DIFFRACTION	r_long_range_B_refined	10.255	41.67	8202
X-RAY DIFFRACTION	r_long_range_B_other	10.255	41.67	8203
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.444→2.507 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.347	168	-
R_work	0.276	2932	-
obs	-	-	90.43 %

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