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- PDB-5k2z: PDX1.3-adduct (Arabidopsis) -

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Basic information

Entry
Database: PDB / ID: 5k2z
TitlePDX1.3-adduct (Arabidopsis)
ComponentsPyridoxal 5'-phosphate synthase subunit PDX1.3
KeywordsBIOSYNTHETIC PROTEIN / pyridoxal 5'-phosphate / vitamin B6 biosynthesis / ribose 5-phosphate
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 / amino acid metabolic process / response to UV-B ...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 / 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
2-azanylpenta-1,4-dien-3-one / Pyridoxal 5'-phosphate synthase subunit PDX1.3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsRobinson, G.C. / Kaufmann, M. / Roux, C. / Fitzpatrick, T.B.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A-141117/1 Switzerland
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural definition of the lysine swing in Arabidopsis thaliana PDX1: Intermediate channeling facilitating vitamin B6 biosynthesis.
Authors: Robinson, G.C. / Kaufmann, M. / Roux, C. / Fitzpatrick, T.B.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Jan 10, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)137,82122
Polymers136,3454
Non-polymers1,47618
Water6,431357
1
C: Pyridoxal 5'-phosphate synthase subunit PDX1.3
D: Pyridoxal 5'-phosphate synthase subunit PDX1.3
hetero molecules

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

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
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)413,46366
Polymers409,03412
Non-polymers4,42854
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation4_445x-1/3,y-2/3,z+1/31
crystal symmetry operation5_445-y-1/3,x-y-2/3,z+1/31
crystal symmetry operation6_445-x+y-1/3,-x-2/3,z+1/31
2
A: Pyridoxal 5'-phosphate synthase subunit PDX1.3
B: 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
hetero molecules

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

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

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

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)413,46366
Polymers409,03412
Non-polymers4,42854
Water21612
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_554x+1/3,y+2/3,z-1/31
crystal symmetry operation8_444-y-2/3,x-y-1/3,z-1/31
crystal symmetry operation9_544-x+y+1/3,-x-1/3,z-1/31
Buried area50190 Å2
ΔGint-601 kcal/mol
Surface area103790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.460, 178.460, 115.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEUAA21 - 29621 - 296
21SERSERLEULEUBB21 - 29621 - 296
12PROPROLEULEUAA22 - 29622 - 296
22PROPROLEULEUCC22 - 29622 - 296
13SERSERLEULEUAA21 - 29621 - 296
23SERSERLEULEUDD21 - 29621 - 296
14PROPROLEULEUBB22 - 29622 - 296
24PROPROLEULEUCC22 - 29622 - 296
15LYSLYSASNASNBB20 - 29720 - 297
25LYSLYSASNASNDD20 - 29720 - 297
16PROPROLEULEUCC22 - 29622 - 296
26PROPROLEULEUDD22 - 29622 - 296

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pyridoxal 5'-phosphate synthase subunit PDX1.3 / PLP synthase subunit PDX1.3


Mass: 34086.184 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)

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Non-polymers , 5 types, 375 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-6R3 / 2-azanylpenta-1,4-dien-3-one


Mass: 97.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H7NO
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM MES.OH pH 6.5, 0.7 M ammonium sulfate, 5% 1,4-dioxane, 10 mM Tris.HCl pH 6.5, 0.1 M potassium chloride, and 5 mM dithiothreitol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97858 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97858 Å / Relative weight: 1
ReflectionResolution: 1.761→92.68 Å / Num. obs: 135507 / % possible obs: 99.5 % / Redundancy: 5.7 % / Rsym value: 0.087 / Net I/av σ(I): 5.575 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.761-1.865.20.8820.8199.2
1.86-1.975.80.5661.3199.7
1.97-2.15.40.3112.3199.2
2.1-2.2760.2013.5199.9
2.27-2.495.60.1384.8199.6
2.49-2.785.80.1065.7199.7
2.78-3.225.80.0817.1199.5
3.22-3.9460.069.9199.8
3.94-5.575.80.05410.8199.6
5.57-44.6156.10.03713.2199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.53 Å44.62 Å
Translation4.53 Å44.62 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASER2.5.7phasing
REFMACrefinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NV2

2nv2


Resolution: 1.8→92.68 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.133 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.101
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 6292 5 %RANDOM
Rwork0.1803 ---
obs0.1814 120693 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 107.53 Å2 / Biso mean: 31.446 Å2 / Biso min: 13.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å2-0.82 Å2-0 Å2
2---1.64 Å20 Å2
3---5.32 Å2
Refinement stepCycle: final / Resolution: 1.8→92.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8302 0 86 357 8745
Biso mean--50.01 30.49 -
Num. residues----1109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198578
X-RAY DIFFRACTIONr_bond_other_d0.0050.028473
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9711561
X-RAY DIFFRACTIONr_angle_other_deg1.167319375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67651125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.94123.531371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.026151496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4191584
X-RAY DIFFRACTIONr_chiral_restr0.0820.21322
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029842
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021922
X-RAY DIFFRACTIONr_mcbond_it3.1532.8184470
X-RAY DIFFRACTIONr_mcbond_other3.1542.8174469
X-RAY DIFFRACTIONr_mcangle_it4.1074.2095593
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A348000.05
12B348000.05
21A344700.05
22C344700.05
31A347600.05
32D347600.05
41B347040.05
42C347040.05
51B351300.04
52D351300.04
61C345700.04
62D345700.04
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 449 -
Rwork0.302 8921 -
all-9370 -
obs--99.67 %

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