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- PDB-6hxg: PDX1.2/PDX1.3 complex (intermediate) -

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Basic information

Entry
Database: PDB / ID: 6hxg
TitlePDX1.2/PDX1.3 complex (intermediate)
Components
  • Pyridoxal 5'-phosphate synthase subunit PDX1.3
  • Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
KeywordsPLANT PROTEIN / Swinging arm lysine / Vitamin B6 / Pseudoenzyme / Reaction intermediate
Function / homology
Function and homology information


response to non-ionic osmotic stress / amine-lyase activity / 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 / amino acid metabolic process ...response to non-ionic osmotic stress / amine-lyase activity / 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 / amino acid metabolic process / response to UV-B / 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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Pyridoxal 5'-phosphate synthase subunit PDX1.3 / Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRobinson, G.C. / Kaufmann, M. / Roux, C. / Martinez-Font, J. / Hothorn, M. / Thore, S. / Fitzpatrick, T.B.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A-141117/1 Switzerland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structure of the pseudoenzyme PDX1.2 in complex with its cognate enzyme PDX1.3: a total eclipse.
Authors: Robinson, G.C. / Kaufmann, M. / Roux, C. / Martinez-Font, J. / Hothorn, M. / Thore, S. / Fitzpatrick, T.B.
History
DepositionOct 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
C: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
E: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
G: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
B: Pyridoxal 5'-phosphate synthase subunit PDX1.3
D: Pyridoxal 5'-phosphate synthase subunit PDX1.3
F: Pyridoxal 5'-phosphate synthase subunit PDX1.3
H: Pyridoxal 5'-phosphate synthase subunit PDX1.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,39316
Polymers255,6258
Non-polymers7698
Water3,909217
1
A: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
G: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
B: Pyridoxal 5'-phosphate synthase subunit PDX1.3
H: Pyridoxal 5'-phosphate synthase subunit PDX1.3
hetero molecules

A: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
G: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
B: Pyridoxal 5'-phosphate synthase subunit PDX1.3
H: Pyridoxal 5'-phosphate synthase subunit PDX1.3
hetero molecules

A: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
G: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
B: Pyridoxal 5'-phosphate synthase subunit PDX1.3
H: Pyridoxal 5'-phosphate synthase subunit PDX1.3
hetero molecules

C: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
E: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
D: Pyridoxal 5'-phosphate synthase subunit PDX1.3
F: Pyridoxal 5'-phosphate synthase subunit PDX1.3
hetero molecules

C: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
E: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
D: Pyridoxal 5'-phosphate synthase subunit PDX1.3
F: Pyridoxal 5'-phosphate synthase subunit PDX1.3
hetero molecules

C: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
E: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
D: Pyridoxal 5'-phosphate synthase subunit PDX1.3
F: Pyridoxal 5'-phosphate synthase subunit PDX1.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)769,18048
Polymers766,87424
Non-polymers2,30624
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_785-y+2,x-y+3,z1
crystal symmetry operation3_475-x+y-1,-x+2,z1
crystal symmetry operation7_544x+1/3,y-1/3,z-1/31
crystal symmetry operation8_784-y+7/3,x-y+11/3,z-1/31
crystal symmetry operation9_364-x+y-5/3,-x+5/3,z-1/31
Unit cell
Length a, b, c (Å)177.976, 177.976, 116.855
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 / AtPDX1 / 3


Mass: 34703.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PDX12, A37, PDX1L2, At3g16050, MSL1.3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 (RIL) / References: UniProt: Q9ZNR6
#2: Protein
Pyridoxal 5'-phosphate synthase subunit PDX1.3 / PLP synthase subunit PDX1.3


Mass: 29202.814 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 BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: Q8L940, pyridoxal 5'-phosphate synthase (glutamine hydrolysing)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.15 % / Description: Rhombohedral morphology
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.8 M ammonium sulphate, 0.05 M MES.OH, pH 6.5, 5% 1,4-dioxane, 0.013 M ammonium sulphate, 0.003 M R5P, 0.001 M G3P, 0.02 M Tris.HCl, pH 8.0, 0.1 M KCl, 0.005 M DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.84→93.12 Å / Num. obs: 119464 / % possible obs: 99.4 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.087 / Rrim(I) all: 0.149 / Net I/σ(I): 8.1
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 5.2 % / Rmerge(I) obs: 2.143 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5824 / CC1/2: 0.085 / Rpim(I) all: 1.502 / Rrim(I) all: 2.639 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
MOSFLM7.2.0data reduction
Aimless7.0.013data scaling
PHASER7.0.013phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chainsaw model derived from 5K3V

5k3v


Resolution: 1.9→93.12 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.938 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 5782 5.3 %RANDOM
Rwork0.2163 ---
obs0.2171 102475 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.71 Å2 / Biso mean: 29.775 Å2 / Biso min: 14.55 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å2-0.64 Å20 Å2
2---1.27 Å20 Å2
3---4.12 Å2
Refinement stepCycle: final / Resolution: 1.9→93.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14726 0 40 217 14983
Biso mean--49.76 30.92 -
Num. residues----2078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01914949
X-RAY DIFFRACTIONr_bond_other_d00.0214159
X-RAY DIFFRACTIONr_angle_refined_deg0.6871.9620290
X-RAY DIFFRACTIONr_angle_other_deg0.5332250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.43952055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.99224.073550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.892152236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7861594
X-RAY DIFFRACTIONr_chiral_restr0.040.22440
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02117350
X-RAY DIFFRACTIONr_gen_planes_other00.023192
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 432 -
Rwork0.341 7583 -
all-8015 -
obs--99.81 %

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