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- PDB-7nhf: Crystal structure of Arabidopsis thaliana Pdx1K166R -

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Basic information

Entry
Database: PDB / ID: 7nhf
TitleCrystal structure of Arabidopsis thaliana Pdx1K166R
ComponentsPyridoxal 5'-phosphate synthase subunit PDX1.3
KeywordsLYASE / VITAMIN B6 BIOSYTHESIS / PLP SYNTHASE / PDX1
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 / FOURIER SYNTHESIS / Resolution: 2.35 Å
AuthorsRodrigues, M.J. / Zhang, Y. / Bolton, R. / Evans, G. / Giri, N. / Royant, A. / Begley, T. / Ealick, S.E. / Tews, I.
CitationJournal: Rsc Chem Biol / Year: 2022
Title: Trapping and structural characterisation of a covalent intermediate in vitamin B 6 biosynthesis catalysed by the Pdx1 PLP synthase.
Authors: Rodrigues, M.J. / Giri, N. / Royant, A. / Zhang, Y. / Bolton, R. / Evans, G. / Ealick, S.E. / Begley, T. / Tews, I.
History
DepositionFeb 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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)125,2208
Polymers124,8404
Non-polymers3804
Water68538
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)375,66124
Polymers374,52112
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 area40750 Å2
ΔGint-244 kcal/mol
Surface area102870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.001, 178.001, 115.127
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
11SERSERLEULEUAA22 - 28821 - 287
21SERSERLEULEUBB22 - 28821 - 287
12LYSLYSSERSERAA21 - 28520 - 284
22LYSLYSSERSERCC21 - 28520 - 284
13PROPROLEULEUAA23 - 28822 - 287
23PROPROLEULEUDD23 - 28822 - 287
14SERSERSERSERBB22 - 28521 - 284
24SERSERSERSERCC22 - 28521 - 284
15PROPROLEULEUBB23 - 28822 - 287
25PROPROLEULEUDD23 - 28822 - 287
16PROPROSERSERCC23 - 28522 - 284
26PROPROSERSERDD23 - 28522 - 284

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 31210.072 Da / Num. of mol.: 4 / Mutation: K166R
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


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


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 28.1% PEG 1000 (w/v) and 100 mM HEPES pH 7.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.980023 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980023 Å / Relative weight: 1
ReflectionResolution: 2.35→38.38 Å / Num. obs: 55906 / % possible obs: 98.7 % / Redundancy: 2.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.079 / Rrim(I) all: 0.138 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.35-2.422.51.0331072343660.6490.7791.3011.394.4
9.97-38.382.90.07320487160.9860.0490.0889.896.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LNU

5lnu


Resolution: 2.35→38.38 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 16.028 / SU ML: 0.314 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2796 5 %RANDOM
Rwork0.2195 ---
obs0.221 53102 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.68 Å2 / Biso mean: 52.542 Å2 / Biso min: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.74 Å2-2.37 Å20 Å2
2---4.74 Å20 Å2
3---15.38 Å2
Refinement stepCycle: final / Resolution: 2.35→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7870 0 20 38 7928
Biso mean--84.33 41.11 -
Num. residues----1072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138046
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177694
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.63210894
X-RAY DIFFRACTIONr_angle_other_deg1.281.57517666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42351078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.18920.86407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.928151320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2071575
X-RAY DIFFRACTIONr_chiral_restr0.0640.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021690
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A79920.06
12B79920.06
21A79220.06
22C79220.06
31A79600.06
32D79600.06
41B78880.04
42C78880.04
51B78680.05
52D78680.05
61C78470.04
62D78470.04
LS refinement shellResolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 196 -
Rwork0.409 3692 -
all-3888 -
obs--93.44 %

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