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- PDB-7nhe: Crystal structure of Arabidopsis thaliana Pdx1K166R-I333 complex -

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Basic information

Entry
Database: PDB / ID: 7nhe
TitleCrystal structure of Arabidopsis thaliana Pdx1K166R-I333 complex
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 / amino acid metabolic process / response to UV-B / response to salt stress ...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 / amino acid metabolic process / response to UV-B / response to salt stress / endomembrane system / 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
Chem-KPR / PHOSPHATE ION / Pyridoxal 5'-phosphate synthase subunit PDX1.3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.23 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 / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)126,00112
Polymers124,8404
Non-polymers1,1608
Water7,837435
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)378,00236
Polymers374,52112
Non-polymers3,48124
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)177.973, 177.973, 115.121
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.502052, -0.864828, -0.003946), (0.864819, 0.502066, -0.004235), (0.005644, -0.001286, 0.999983)0.06596, -0.10943, 0.0513
3given(-0.989735, -0.142853, 0.004106), (-0.142843, 0.989742, 0.002572), (-0.004431, 0.001959, -0.999988)0.35655, 0.14713, -76.840973
4given(-0.370975, -0.928638, 0.003082), (-0.928643, 0.370976, -0.000463), (-0.000714, -0.003034, -0.999995)0.22638, -0.00106, -76.899071

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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: isolated from a natural source / Formula: PO4
#3: Chemical
ChemComp-KPR / [(~{E},4~{S})-4-azanyl-3-oxidanylidene-pent-1-enyl] dihydrogen phosphate


Mass: 195.110 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C5H10NO5P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 28.1% PEG 1000 (w/v) and 100 mM HEPES pH 7.0

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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 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980023 Å / Relative weight: 1
ReflectionResolution: 2.23→92.23 Å / Num. obs: 66508 / % possible obs: 99.7 % / Redundancy: 3.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.059 / Rrim(I) all: 0.12 / Net I/σ(I): 7.2 / Num. measured all: 260302 / Scaling rejects: 441
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
2.23-2.283.80.8861711344750.5170.5341.042.499.8
10.44-92.234.20.05926976400.9570.0350.0716.799.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
Cootmodel building
DIALSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LNU

5lnu


Resolution: 2.23→92.23 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 3316 5 %RANDOM
Rwork0.1752 62998 --
obs0.1774 66314 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.53 Å2 / Biso mean: 48.4446 Å2 / Biso min: 28.44 Å2
Refinement stepCycle: final / Resolution: 2.23→92.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8119 0 68 435 8622
Biso mean--60.08 44.07 -
Num. residues----1084
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.23-2.260.30771380.27522594273299
2.26-2.290.32641370.25782666280399
2.29-2.330.30831440.25322574271899
2.33-2.360.24391270.23512621274899
2.36-2.410.25461420.23322630277299
2.41-2.450.2531470.21592608275599
2.45-2.50.24151470.210126602807100
2.5-2.550.2411380.20922610274899
2.55-2.60.24591490.20422580272999
2.6-2.660.26581430.19462645278899
2.66-2.730.22121340.18692601273599
2.73-2.80.26431280.18482640276899
2.8-2.890.24741390.18842636277599
2.89-2.980.25471350.187626372772100
2.98-3.090.22631230.192326232746100
3.09-3.210.24981430.188226612804100
3.21-3.350.23911290.178926222751100
3.36-3.530.22121270.170826422769100
3.53-3.750.21381500.16382605275599
3.75-4.040.19711450.148826542799100
4.04-4.450.17451470.135326102757100
4.45-5.090.16491260.14472642276899
5.1-6.420.2131470.176926372784100
6.42-92.230.18291310.13982600273199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1116-0.0248-0.08980.3067-0.24620.6-0.0202-0.138-0.11970.1138-0.0221-0.0603-0.0668-0.01810.04120.28120.0008-0.02220.21870.04830.761614.7798-35.6248-16.176
20.8028-0.43810.13940.9119-0.1960.5407-0.0919-0.1454-0.11070.20630.09450.1619-0.0127-0.0608-0.00020.27330.01630.05780.25530.0530.8201-23.3027-30.6973-16.2605
31.662-0.04010.49440.5510.01970.9498-0.00380.3288-0.1963-0.1295-0.00490.02860.06970.06550.01040.26630.0025-0.00770.3108-0.11960.7873-9.6427-37.3681-60.5992
40.5310.4575-0.18390.95780.22440.4268-0.07270.173-0.0914-0.22430.0465-0.1228-0.048-0.0240.0250.28220.03110.0670.2968-0.04910.748227.5168-26.8479-60.6487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 21:301)A21 - 301
2X-RAY DIFFRACTION2(chain B and resseq 22:301)B22 - 301
3X-RAY DIFFRACTION3(chain C and resseq 21:301)C21 - 301
4X-RAY DIFFRACTION4(chain D and resseq 23:301)D23 - 301

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