PDB-8s2w: SSX structure of Arabidopsis thaliana Pdx1.3 grown in seeded batc...

ID or keywords:

Entry

Database: PDB / ID: 8s2w

Title

SSX structure of Arabidopsis thaliana Pdx1.3 grown in seeded batch conditions

Components

Pyridoxal 5'-phosphate synthase subunit PDX1.3

Keywords

LYASE / Vitamin B6

Function / homology

Function and homology information

response to non-ionic osmotic stress / response to lipid hydroperoxide / chlorophyll metabolic process / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / hyperosmotic salinity response / pyridoxal phosphate biosynthetic process / amino acid metabolic process / response to UV-B / response to salt stress ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Stubbs, J. / Tews, I. / Maly, M.

Funding support

United Kingdom, 2items

Organization	Grant number	Country
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/S008470/1	United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/T008768/1	United Kingdom

Citation

Journal: Iucrj / Year: 2024
Title: Droplet microfluidics for time-resolved serial crystallography.
Authors: Stubbs, J. / Hornsey, T. / Hanrahan, N. / Esteban, L.B. / Bolton, R. / Maly, M. / Basu, S. / Orlans, J. / de Sanctis, D. / Shim, J.U. / Shaw Stewart, P.D. / Orville, A.M. / Tews, I. / West, J.

History

Deposition	Feb 19, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 28, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2024	Group: Database references / Category: citation / citation_author

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8s2w.cif.gz	218.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8s2w.ent.gz	170.1 KB	Display	PDB format
PDBx/mmJSON format	8s2w.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8s2w_validation.pdf.gz	456 KB	Display	wwPDB validaton report
Full document	8s2w_full_validation.pdf.gz	461.8 KB	Display
Data in XML	8s2w_validation.xml.gz	38.1 KB	Display
Data in CIF	8s2w_validation.cif.gz	53 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s2/8s2w ftp://data.pdbj.org/pub/pdb/validation_reports/s2/8s2w	HTTPS FTP

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Related structure data

Related structure data	8s2uC 8s2vC 8s2xC 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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Pyridoxal 5'-phosphate synthase subunit PDX1.3

B: Pyridoxal 5'-phosphate synthase subunit PDX1.3

C: Pyridoxal 5'-phosphate synthase subunit PDX1.3

D: Pyridoxal 5'-phosphate synthase subunit PDX1.3

hetero molecules

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

1

A: Pyridoxal 5'-phosphate synthase subunit PDX1.3

B: Pyridoxal 5'-phosphate synthase subunit PDX1.3

C: Pyridoxal 5'-phosphate synthase subunit PDX1.3

D: Pyridoxal 5'-phosphate synthase subunit PDX1.3

hetero molecules

A: Pyridoxal 5'-phosphate synthase subunit PDX1.3

B: Pyridoxal 5'-phosphate synthase subunit PDX1.3

C: Pyridoxal 5'-phosphate synthase subunit PDX1.3

D: Pyridoxal 5'-phosphate synthase subunit PDX1.3

hetero molecules

A: Pyridoxal 5'-phosphate synthase subunit PDX1.3

B: Pyridoxal 5'-phosphate synthase subunit PDX1.3

C: Pyridoxal 5'-phosphate synthase subunit PDX1.3

D: Pyridoxal 5'-phosphate synthase subunit PDX1.3

hetero molecules

defined by author&software
Evidence: gel filtration
375 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	177.9, 177.9, 117.3
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	146
Space group name H-M	H3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 22 - 289 / Label seq-ID: 21 - 288

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Pyridoxal 5'-phosphate synthase subunit PDX1.3 / AtPDX1.3 / AtPDX1 / 1 / PLP synthase subunit PDX1.3 Mass: 31182.057 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PDX13, GIP2, PDX1L3, RSR4, At5g01410, T10O8.120 / Production host: Escherichia coli (E. coli) References: UniProt: Q8L940, pyridoxal 5'-phosphate synthase (glutamine hydrolysing)
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 57.05 %
Crystal grow	Temperature: 294 K / Method: batch mode / pH: 7 / Details: 600 mM Sodium citrate and 100 mM HEPES pH 7

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Data collection

Diffraction	Mean temperature: 293 K / Serial crystal experiment: Y
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07 Å
Detector	Type: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Jan 26, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.07 Å / Relative weight: 1
Reflection	Resolution: 2.5→93.33 Å / Num. obs: 47878 / % possible obs: 100 % / Redundancy: 47.4 % / B_iso Wilson estimate: 49.36 Å² / CC_1/2: 0.96 / CC star: 0.99 / Net I/σ(I): 4.4
Reflection shell	Resolution: 2.5→2.54 Å / Redundancy: 45.18 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4703 / CC_1/2: 0.17 / CC star: 0.54 / % possible all: 100
Serial crystallography sample delivery	Description: SOS Chip / Method: fixed target
Serial crystallography data reduction	Crystal hits: 20268 / Frames indexed: 19325 / Frames total: 245400

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
CrystFEL	0.10.2	data reduction
CrystFEL	0.10.2	data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→64.472 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.961 / WR_factor R_free: 0.171 / WR_factor R_work: 0.144 / SU B: 12.573 / SU ML: 0.233 / Average fsc free: 0.9497 / Average fsc work: 0.9585 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.21
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1934	2316	4.838 %	RANDOM
R_work	0.1676	45557	-	-
all	0.169	-	-	-
obs	-	47873	99.994 %	-

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: 59.434 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.005 Å²	-0.002 Å²	0 Å²
2-	-	-0.005 Å²	0 Å²
3-	-	-	0.016 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→64.472 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8056	0	20	181	8257

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	8208
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8108
X-RAY DIFFRACTION	r_angle_refined_deg	1.407	1.814	11079
X-RAY DIFFRACTION	r_angle_other_deg	0.458	1.76	18562
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.304	5	1074
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.892	5	80
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.18	10	1433
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.129	10	358
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	1272
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	9902
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1858
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	1739
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.199	0.2	7812
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	4127
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	4597
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	201
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.157	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.152	0.2	84
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.141	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	4.34	5.61	4299
X-RAY DIFFRACTION	r_mcbond_other	4.339	5.609	4298
X-RAY DIFFRACTION	r_mcangle_it	6.57	10.076	5372
X-RAY DIFFRACTION	r_mcangle_other	6.57	10.077	5373
X-RAY DIFFRACTION	r_scbond_it	5.847	6.203	3909
X-RAY DIFFRACTION	r_scbond_other	5.714	6.191	3894
X-RAY DIFFRACTION	r_scangle_it	9.179	11.139	5707
X-RAY DIFFRACTION	r_scangle_other	9.099	11.118	5684
X-RAY DIFFRACTION	r_lrange_it	11.006	53.031	8883
X-RAY DIFFRACTION	r_lrange_other	11.013	52.954	8863
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.062	0.05	8409
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.061	0.05	8418
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.064	0.05	8400
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.059	0.05	8408
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.07	0.05	8381
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.07	0.05	8374

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.06218	0.05011
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06218	0.05011
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06117	0.05011
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06117	0.05011
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06418	0.05011
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06418	0.05011
4	7	A	X-RAY DIFFRACTION	Local ncs	0.05898	0.05011
4	8	A	X-RAY DIFFRACTION	Local ncs	0.05898	0.05011
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07044	0.05011
5	10	A	X-RAY DIFFRACTION	Local ncs	0.07044	0.05011
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06959	0.05011
6	12	A	X-RAY DIFFRACTION	Local ncs	0.06959	0.05011

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
2.5-2.565	0.355	166	0.376	3359	0.375	3525	0.907	0.896	100	0.372
2.565-2.635	0.42	151	0.368	3317	0.37	3469	0.866	0.899	99.9712	0.363
2.635-2.711	0.377	172	0.343	3138	0.345	3310	0.888	0.913	100	0.332
2.711-2.795	0.344	135	0.318	3164	0.319	3299	0.924	0.927	100	0.309
2.795-2.886	0.315	150	0.297	3009	0.298	3159	0.927	0.94	100	0.282
2.886-2.987	0.293	135	0.267	2891	0.268	3026	0.941	0.953	100	0.245
2.987-3.1	0.239	185	0.239	2764	0.239	2949	0.962	0.962	100	0.216
3.1-3.226	0.241	207	0.204	2679	0.207	2886	0.954	0.973	100	0.179
3.226-3.369	0.211	120	0.168	2554	0.17	2674	0.973	0.982	100	0.146
3.369-3.533	0.18	101	0.147	2501	0.149	2602	0.976	0.987	100	0.132
3.533-3.723	0.163	152	0.134	2308	0.136	2460	0.984	0.989	100	0.119
3.723-3.948	0.16	122	0.118	2249	0.12	2371	0.984	0.992	100	0.107
3.948-4.22	0.13	87	0.1	2101	0.102	2188	0.988	0.994	100	0.093
4.22-4.556	0.114	101	0.087	1951	0.089	2052	0.991	0.995	100	0.083
4.556-4.989	0.119	103	0.084	1789	0.086	1892	0.992	0.996	100	0.08
4.989-5.573	0.115	84	0.102	1607	0.103	1691	0.991	0.994	100	0.096
5.573-6.428	0.188	42	0.133	1480	0.134	1522	0.979	0.99	100	0.126
6.428-7.853	0.177	41	0.131	1225	0.133	1266	0.98	0.99	100	0.133
7.853-11.024	0.128	56	0.111	926	0.111	982	0.99	0.993	100	0.126
11.024-64.472	0.169	6	0.187	547	0.187	553	0.983	0.978	100	0.213

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