PDB-8s2x: SSX structure of Arabidopsis thaliana Pdx1.3 grown in microfluidi...

ID or keywords:

Entry

Database: PDB / ID: 8s2x

Title

SSX structure of Arabidopsis thaliana Pdx1.3 grown in microfluidic droplets

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 / pyridoxal phosphate biosynthetic process / hyperosmotic salinity response / pyridoxine biosynthetic process / response to UV-B / amino acid metabolic process ...
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

-
Download

PDBx/mmCIF format	8s2x.cif.gz	221.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8s2x.ent.gz	172.6 KB	Display	PDB format
PDBx/mmJSON format	8s2x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s2/8s2x ftp://data.pdbj.org/pub/pdb/validation_reports/s2/8s2x	HTTPS FTP

-
Related structure data

Related structure data	8s2uC 8s2vC 8s2wC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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

126 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
378 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	180.3, 180.3, 119.2
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 / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	22 - 289	21 - 288
2	1	1	GLY	GLY	22 - 289	21 - 288
3	2	2	LEU	LEU	22 - 288	21 - 287
4	2	2	LEU	LEU	22 - 288	21 - 287
5	3	3	GLU	GLU	22 - 290	21 - 289
6	3	3	GLU	GLU	22 - 290	21 - 289
7	4	4	LEU	LEU	22 - 288	21 - 287
8	4	4	LEU	LEU	22 - 288	21 - 287
9	5	5	GLY	GLY	22 - 289	21 - 288
10	5	5	GLY	GLY	22 - 289	21 - 288
11	6	6	LEU	LEU	22 - 288	21 - 287
12	6	6	LEU	LEU	22 - 288	21 - 287

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-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.86 %
Crystal grow	Temperature: 294 K / Method: microfluidic / pH: 7 / Details: 600 mM Sodium citrate and 100 mM HEPES pH 7

-
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→94.75 Å / Num. obs: 50011 / % possible obs: 100 % / Redundancy: 44.2 % / B_iso Wilson estimate: 45.27 Å² / CC_1/2: 0.96 / CC star: 0.99 / Net I/σ(I): 5
Reflection shell	Resolution: 2.5→2.54 Å / Redundancy: 44.2 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4635 / CC_1/2: 0.27 / CC star: 0.65 / % possible all: 100
Serial crystallography sample delivery	Description: SOS Chip / Method: fixed target
Serial crystallography data reduction	Crystal hits: 20827 / Frames indexed: 20635 / Frames total: 245400

-
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→65.396 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.959 / WR_factor R_free: 0.173 / WR_factor R_work: 0.141 / SU B: 10.207 / SU ML: 0.197 / Average fsc free: 0.9601 / Average fsc work: 0.9676 / Cross valid method: FREE R-VALUE / ESU R: 0.312 / ESU R Free: 0.201
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1883	2510	5.02 %
R_work	0.1584	47493	-
all	0.16	-	-
obs	-	50003	99.984 %

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: 59.187 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.006 Å²	0.003 Å²	0 Å²
2-	-	0.006 Å²	-0 Å²
3-	-	-	-0.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→65.396 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8088	0	72	186	8346

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	8294
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8155
X-RAY DIFFRACTION	r_angle_refined_deg	1.511	1.815	11198
X-RAY DIFFRACTION	r_angle_other_deg	0.504	1.76	18676
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.5	5	1080
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.081	5	82
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.633	10	1442
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.104	10	362
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	1280
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	10004
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1868
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	1548
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.195	0.2	7110
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	4080
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	4502
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	160
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.14	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.162	0.2	64
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.107	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	4.956	5.585	4314
X-RAY DIFFRACTION	r_mcbond_other	4.956	5.587	4315
X-RAY DIFFRACTION	r_mcangle_it	7.523	10.04	5390
X-RAY DIFFRACTION	r_mcangle_other	7.523	10.042	5391
X-RAY DIFFRACTION	r_scbond_it	6.193	6.221	3980
X-RAY DIFFRACTION	r_scbond_other	6.109	6.207	3961
X-RAY DIFFRACTION	r_scangle_it	9.728	11.171	5806
X-RAY DIFFRACTION	r_scangle_other	9.702	11.149	5783
X-RAY DIFFRACTION	r_lrange_it	11.962	51.06	8662
X-RAY DIFFRACTION	r_lrange_other	11.951	51.085	8637
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.06	0.05	8047
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.063	0.05	8026
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.078	0.05	8021
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.059	0.05	8110
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.07	0.05	8076
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.075	0.05	7982

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	0.06014	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06014	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06336	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06336	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07835	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07835	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.05879	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.05879	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07024	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.07024	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.07529	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.07529	0.0501

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	0.352	209	0.348	3519	0.348	3730	0.905	0.905	99.9464	0.341
2.565-2.635	0.311	157	0.317	3438	0.317	3596	0.932	0.929	99.9722	0.306
2.635-2.711	0.347	136	0.295	3359	0.297	3497	0.911	0.938	99.9428	0.279
2.711-2.795	0.249	162	0.257	3253	0.256	3415	0.959	0.957	100	0.234
2.795-2.886	0.271	139	0.252	3116	0.253	3255	0.949	0.958	100	0.229
2.886-2.987	0.274	146	0.236	3070	0.237	3216	0.946	0.964	100	0.211
2.987-3.1	0.249	184	0.223	2884	0.225	3068	0.959	0.969	100	0.198
3.1-3.226	0.258	188	0.19	2783	0.194	2972	0.957	0.977	99.9664	0.167
3.226-3.369	0.234	140	0.172	2701	0.175	2841	0.963	0.981	100	0.151
3.369-3.533	0.175	143	0.145	2565	0.146	2708	0.981	0.987	100	0.129
3.533-3.724	0.158	115	0.127	2488	0.128	2603	0.985	0.99	100	0.114
3.724-3.949	0.172	136	0.114	2279	0.116	2415	0.982	0.992	100	0.103
3.949-4.22	0.117	99	0.099	2209	0.1	2308	0.991	0.994	100	0.093
4.22-4.557	0.123	90	0.086	2027	0.088	2117	0.991	0.995	100	0.083
4.557-4.989	0.12	78	0.089	1897	0.09	1975	0.992	0.995	100	0.086
4.989-5.574	0.138	110	0.114	1680	0.116	1790	0.988	0.993	100	0.11
5.574-6.429	0.154	78	0.13	1485	0.132	1563	0.985	0.99	100	0.126
6.429-7.854	0.156	104	0.124	1217	0.127	1321	0.985	0.991	100	0.127
7.854-11.028	0.142	62	0.12	979	0.122	1041	0.989	0.992	100	0.133
11.028-65.396	0.204	34	0.199	544	0.2	578	0.965	0.98	100	0.229

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi