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

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Basic information

Entry
Database: PDB / ID: 8s2w
TitleSSX structure of Arabidopsis thaliana Pdx1.3 grown in seeded batch conditions
ComponentsPyridoxal 5'-phosphate synthase subunit PDX1.3
KeywordsLYASE / 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 / response to UV-B / amino acid metabolic process / endomembrane system ...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 / response to UV-B / amino acid metabolic process / endomembrane system / response to salt stress / response to oxidative stress / protein heterodimerization activity / protein homodimerization activity / plasma membrane / cytosol
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
PHOSPHATE ION / Pyridoxal 5'-phosphate synthase subunit PDX1.3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsStubbs, J. / Tews, I. / Maly, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
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
#1: Journal: BioRxiv / Year: 2024
Title: Droplet microfluidics for time-resolved serial crystallography
Authors: Stubbs, J. / Tews, I. / Maly, M.
History
DepositionFeb 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)125,1088
Polymers124,7284
Non-polymers3804
Water3,261181
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


Theoretical massNumber of molelcules
Total (without water)375,32424
Polymers374,18512
Non-polymers1,14012
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area41450 Å2
ΔGint-225 kcal/mol
Surface area106380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.9, 177.9, 117.3
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

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-IDComponent-IDEns-ID
111
211
322
422
533
633
744
844
955
1055
1166
1266

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

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Components

#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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

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

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Jan 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.5→93.33 Å / Num. obs: 47878 / % possible obs: 100 % / Redundancy: 47.4 % / Biso Wilson estimate: 49.36 Å2 / CC1/2: 0.96 / CC star: 0.99 / Net I/σ(I): 4.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 45.18 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4703 / CC1/2: 0.17 / CC star: 0.54 / % possible all: 100
Serial crystallography sample deliveryDescription: SOS Chip / Method: fixed target
Serial crystallography data reductionCrystal hits: 20268 / Frames indexed: 19325 / Frames total: 245400

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrystFEL0.10.2data reduction
CrystFEL0.10.2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→64.472 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.171 / WRfactor Rwork: 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
RfactorNum. reflection% reflectionSelection details
Rfree0.1934 2316 4.838 %RANDOM
Rwork0.1676 45557 --
all0.169 ---
obs-47873 99.994 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.434 Å2
Baniso -1Baniso -2Baniso -3
1--0.005 Å2-0.002 Å20 Å2
2---0.005 Å20 Å2
3---0.016 Å2
Refinement stepCycle: LAST / Resolution: 2.5→64.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8056 0 20 181 8257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0128208
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168108
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.81411079
X-RAY DIFFRACTIONr_angle_other_deg0.4581.7618562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30451074
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.892580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18101433
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.12910358
X-RAY DIFFRACTIONr_chiral_restr0.0620.21272
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029902
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021858
X-RAY DIFFRACTIONr_nbd_refined0.2130.21739
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.27812
X-RAY DIFFRACTIONr_nbtor_refined0.1730.24127
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.24597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2201
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1570.29
X-RAY DIFFRACTIONr_nbd_other0.1520.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.216
X-RAY DIFFRACTIONr_mcbond_it4.345.614299
X-RAY DIFFRACTIONr_mcbond_other4.3395.6094298
X-RAY DIFFRACTIONr_mcangle_it6.5710.0765372
X-RAY DIFFRACTIONr_mcangle_other6.5710.0775373
X-RAY DIFFRACTIONr_scbond_it5.8476.2033909
X-RAY DIFFRACTIONr_scbond_other5.7146.1913894
X-RAY DIFFRACTIONr_scangle_it9.17911.1395707
X-RAY DIFFRACTIONr_scangle_other9.09911.1185684
X-RAY DIFFRACTIONr_lrange_it11.00653.0318883
X-RAY DIFFRACTIONr_lrange_other11.01352.9548863
X-RAY DIFFRACTIONr_ncsr_local_group_10.0620.058409
X-RAY DIFFRACTIONr_ncsr_local_group_20.0610.058418
X-RAY DIFFRACTIONr_ncsr_local_group_30.0640.058400
X-RAY DIFFRACTIONr_ncsr_local_group_40.0590.058408
X-RAY DIFFRACTIONr_ncsr_local_group_50.070.058381
X-RAY DIFFRACTIONr_ncsr_local_group_60.070.058374
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.062180.05011
12AX-RAY DIFFRACTIONLocal ncs0.062180.05011
23AX-RAY DIFFRACTIONLocal ncs0.061170.05011
24AX-RAY DIFFRACTIONLocal ncs0.061170.05011
35AX-RAY DIFFRACTIONLocal ncs0.064180.05011
36AX-RAY DIFFRACTIONLocal ncs0.064180.05011
47AX-RAY DIFFRACTIONLocal ncs0.058980.05011
48AX-RAY DIFFRACTIONLocal ncs0.058980.05011
59AX-RAY DIFFRACTIONLocal ncs0.070440.05011
510AX-RAY DIFFRACTIONLocal ncs0.070440.05011
611AX-RAY DIFFRACTIONLocal ncs0.069590.05011
612AX-RAY DIFFRACTIONLocal ncs0.069590.05011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.5-2.5650.3551660.37633590.37535250.9070.8961000.372
2.565-2.6350.421510.36833170.3734690.8660.89999.97120.363
2.635-2.7110.3771720.34331380.34533100.8880.9131000.332
2.711-2.7950.3441350.31831640.31932990.9240.9271000.309
2.795-2.8860.3151500.29730090.29831590.9270.941000.282
2.886-2.9870.2931350.26728910.26830260.9410.9531000.245
2.987-3.10.2391850.23927640.23929490.9620.9621000.216
3.1-3.2260.2412070.20426790.20728860.9540.9731000.179
3.226-3.3690.2111200.16825540.1726740.9730.9821000.146
3.369-3.5330.181010.14725010.14926020.9760.9871000.132
3.533-3.7230.1631520.13423080.13624600.9840.9891000.119
3.723-3.9480.161220.11822490.1223710.9840.9921000.107
3.948-4.220.13870.121010.10221880.9880.9941000.093
4.22-4.5560.1141010.08719510.08920520.9910.9951000.083
4.556-4.9890.1191030.08417890.08618920.9920.9961000.08
4.989-5.5730.115840.10216070.10316910.9910.9941000.096
5.573-6.4280.188420.13314800.13415220.9790.991000.126
6.428-7.8530.177410.13112250.13312660.980.991000.133
7.853-11.0240.128560.1119260.1119820.990.9931000.126
11.024-64.4720.16960.1875470.1875530.9830.9781000.213

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