PDB-8jg7: Serine decarboxylase

ID or keywords:

Entry

Database: PDB / ID: 8jg7

Title

Serine decarboxylase

Components

Serine decarboxylase

Keywords

BIOSYNTHETIC PROTEIN / PLP

Function / homology

Function and homology information

ethanolamine metabolic process / serine decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxylic acid metabolic process / pyridoxal phosphate binding / plasma membrane / cytosol
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Wang, H. / Gong, W.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal structure of aserine decarboxylase from Arabidopsis thaliana
Authors: Wang, H.

History

Deposition	May 19, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 22, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8jg7.cif.gz	327.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8jg7.ent.gz	266.3 KB	Display	PDB format
PDBx/mmJSON format	8jg7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8jg7_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8jg7_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8jg7_validation.xml.gz	57.4 KB	Display
Data in CIF	8jg7_validation.cif.gz	77.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jg/8jg7 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/8jg7	HTTPS FTP

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Related structure data

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

Deposited unit

A: Serine decarboxylase

C: Serine decarboxylase

D: Serine decarboxylase

E: Serine decarboxylase

hetero molecules

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

1

A: Serine decarboxylase

E: Serine decarboxylase

hetero molecules

defined by author&software
95.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Serine decarboxylase

D: Serine decarboxylase

hetero molecules

defined by author&software
95.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	115.360, 149.450, 139.126
Angle α, β, γ (deg.)	90.00, 109.18, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Serine decarboxylase / AtSDC / Protein EMBRYO DEFECTIVE 1075 / Serine decarboxylase 1 / AtSDC1 Mass: 47436.230 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SDC, EMB1075, SDC1, At1g43710, F2J6.7 / Production host: Escherichia coli (E. coli) References: UniProt: Q9MA74, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
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: 2.99 Å³/Da / Density % sol: 58.85 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 400, 0.2M CaCl2, PH8.0

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.85→50 Å / Num. obs: 52125 / % possible obs: 99.6 % / Redundancy: 5.9 % / CC_1/2: 0.86 / CC star: 0.962 / R_merge(I) obs: 0.173 / R_pim(I) all: 0.076 / R_rim(I) all: 0.189 / Χ²: 2.023 / Net I/σ(I): 3.5

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
2.85-2.9	5	0.551	2556	0.846	0.957	0.27	0.616	0.545	98.1
2.9-2.95	5.7	0.549	2617	0.898	0.973	0.252	0.606	0.556	99.9
2.95-3.01	6.2	0.496	2580	0.916	0.978	0.216	0.541	0.561	100
3.01-3.07	6.1	0.421	2595	0.919	0.979	0.184	0.46	0.59	99.9
3.07-3.14	6.2	0.365	2623	0.945	0.986	0.158	0.399	0.732	100
3.14-3.21	6.1	0.325	2605	0.952	0.988	0.141	0.355	0.728	99.9
3.21-3.29	6.1	0.286	2581	0.966	0.991	0.124	0.313	0.707	99.9
3.29-3.38	6.1	0.258	2633	0.964	0.991	0.112	0.282	0.813	100
3.38-3.48	6.1	0.28	2610	0.354	0.723	0.128	0.309	1.118	100
3.48-3.59	6.1	0.185	2587	0.977	0.994	0.08	0.202	1.045	99.9
3.59-3.72	6.1	0.18	2624	0.981	0.995	0.079	0.197	1.141	100
3.72-3.87	6	0.164	2600	0.969	0.992	0.071	0.179	1.508	99.9
3.87-4.04	6	0.162	2583	0.978	0.994	0.071	0.177	1.51	99.7
4.04-4.26	5.9	0.133	2625	0.972	0.993	0.058	0.146	1.793	99.6
4.26-4.52	5.8	0.13	2621	0.964	0.991	0.058	0.143	1.909	99.5
4.52-4.87	5.7	0.116	2579	0.981	0.995	0.052	0.127	1.805	99.7
4.87-5.36	5.2	0.119	2607	0.972	0.993	0.055	0.131	2.523	99.1
5.36-6.14	5.5	0.128	2570	0.961	0.99	0.057	0.141	2.894	98
6.14-7.73	6.5	0.112	2644	0.972	0.993	0.047	0.121	3.101	100
7.73-50	6.4	0.165	2685	0.904	0.975	0.07	0.18	13.552	100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.85→49.39 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.886 / SU B: 16.235 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2618	2576	4.9 %	RANDOM
R_work	0.21353	-	-	-
obs	0.21591	49543	99.42 %	-

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: 55.93 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.32 Å²	-0 Å²	-0.2 Å²
2-	-	-1.58 Å²	0 Å²
3-	-	-	-4.51 Å²

Refinement step

Cycle: 1 / Resolution: 2.85→49.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13000	0	88	0	13088

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	13404
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	12142
X-RAY DIFFRACTION	r_angle_refined_deg	1.41	1.64	18108
X-RAY DIFFRACTION	r_angle_other_deg	0.465	1.558	28291
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.317	5	1624
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	15.831	10	92
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.36	10	2304
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	1944
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	15204
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2728
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	5.064	5.518	6520
X-RAY DIFFRACTION	r_mcbond_other	5.061	5.518	6520
X-RAY DIFFRACTION	r_mcangle_it	7.566	8.252	8136
X-RAY DIFFRACTION	r_mcangle_other	7.565	8.253	8137
X-RAY DIFFRACTION	r_scbond_it	5.377	5.923	6884
X-RAY DIFFRACTION	r_scbond_other	5.375	5.924	6881
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	8.088	8.723	9973
X-RAY DIFFRACTION	r_long_range_B_refined	10.448	69.428	14924
X-RAY DIFFRACTION	r_long_range_B_other	10.448	69.428	14925
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.85→2.916 Å

	R_factor	Num. reflection	% reflection
R_free	0.331	177	-
R_work	0.294	3527	-
obs	-	-	95.98 %

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