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- PDB-6hye: PDX1.2/PDX1.3 complex (PDX1.3:K97A) -

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Basic information

Entry
Database: PDB / ID: 6hye
TitlePDX1.2/PDX1.3 complex (PDX1.3:K97A)
Components
  • Pyridoxal 5'-phosphate synthase subunit PDX1.3
  • Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
KeywordsPLANT PROTEIN / Swinging arm lysine / Pseudoenzyme / Inactive mutant / dodecamer
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 / response to UV-B ...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 / 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 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: 2.53 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 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Derived calculations
Category: database_PDB_remark / struct_conn / struct_conn_type
Item: _database_PDB_remark.text
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)272,37916
Polymers271,6108
Non-polymers7698
Water1,35175
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)817,13748
Polymers814,83124
Non-polymers2,30624
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_544x+1/3,y-1/3,z-1/31
crystal symmetry operation8_554-y+1/3,x-y+2/3,z-1/31
crystal symmetry operation9_444-x+y-2/3,-x-1/3,z-1/31
Unit cell
Length a, b, c (Å)177.460, 177.460, 115.770
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: 33874.504 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) / Variant (production host): RIL / References: UniProt: Q9ZNR6
#2: Protein
Pyridoxal 5'-phosphate synthase subunit PDX1.3 / PLP synthase subunit PDX1.3


Mass: 34028.082 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.58 Å3/Da / Density % sol: 52.44 % / 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, pH 6.5, 5% 1,4-dioxane, 0.01 M Tris, pH 7.0, 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: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.53→92.47 Å / Num. obs: 45389 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.109 / Rrim(I) all: 0.209 / Net I/σ(I): 9
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4481 / CC1/2: 0.639 / Rpim(I) all: 0.616 / Rrim(I) all: 1.159 / % possible all: 100

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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: 2.53→92.47 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.876 / SU B: 29.285 / SU ML: 0.596 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2807 2229 4.9 %RANDOM
Rwork0.2347 ---
obs0.2369 43157 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 154.24 Å2 / Biso mean: 29.321 Å2 / Biso min: 7.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å2-1.03 Å2-0 Å2
2---2.06 Å20 Å2
3---6.68 Å2
Refinement stepCycle: final / Resolution: 2.53→92.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14778 0 40 75 14893
Biso mean--42 23.48 -
Num. residues----2091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01915000
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214152
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.9620357
X-RAY DIFFRACTIONr_angle_other_deg0.555332205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19552068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91923.996553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.99152225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.411597
X-RAY DIFFRACTIONr_chiral_restr0.0520.22443
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217435
X-RAY DIFFRACTIONr_gen_planes_other00.023210
LS refinement shellResolution: 2.53→2.596 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 181 -
Rwork0.37 3157 -
all-3338 -
obs--100 %

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