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- PDB-5lns: Crystal structure of Arabidopsis thaliana Pdx1-R5P complex -

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Basic information

Entry
Database: PDB / ID: 5lns
TitleCrystal structure of Arabidopsis thaliana Pdx1-R5P complex
ComponentsPyridoxal 5'-phosphate synthase subunit PDX1.3
KeywordsLYASE / beta/alpha barrel / pyridoxal phosphate synthase / glutamine amidotransferase / vitamin B6 biosynthesis
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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
RIBULOSE-5-PHOSPHATE / PHOSPHATE ION / Pyridoxal 5'-phosphate synthase subunit PDX1.3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.91 Å
AuthorsRodrigues, M.J. / Windeisen, V. / Zhang, Y. / Guedez, G. / Weber, S. / Strohmeier, M. / Hanes, J.W. / Royant, A. / Evans, G. / Sinning, I. ...Rodrigues, M.J. / Windeisen, V. / Zhang, Y. / Guedez, G. / Weber, S. / Strohmeier, M. / Hanes, J.W. / Royant, A. / Evans, G. / Sinning, I. / Ealick, S.E. / Begley, T.P. / Tews, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationTE368 Germany
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis.
Authors: Rodrigues, M.J. / Windeisen, V. / Zhang, Y. / Guedez, G. / Weber, S. / Strohmeier, M. / Hanes, J.W. / Royant, A. / Evans, G. / Sinning, I. / Ealick, S.E. / Begley, T.P. / Tews, I.
History
DepositionAug 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Oct 16, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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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)138,16212
Polymers136,8614
Non-polymers1,3008
Water15,475859
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)414,48536
Polymers410,58412
Non-polymers3,90124
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 area49100 Å2
ΔGint-172 kcal/mol
Surface area99100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.728, 176.728, 114.646
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 subunit PDX1.3 / PLP synthase subunit PDX1.3


Mass: 34215.297 Da / Num. of mol.: 4 / Fragment: PLP synthase subunit Pdx1.3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PDX13, GIP2, PDX1L3, RSR4, At5g01410, T10O8.120 / Plasmid: pET-21a-d(+) / Details (production host): NdeI/XhoI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8L940, pyridoxal 5'-phosphate synthase (glutamine hydrolysing)
#2: Sugar
ChemComp-5RP / RIBULOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H11O8P
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 859 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.51 % / Mosaicity: 0.423 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH7.5, 0.5 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2008 / Details: torodial focusing mirrors
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.91→25 Å / Num. obs: 103410 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.27 Å2 / Rmerge(I) obs: 0.056 / Net I/av σ(I): 15.192 / Net I/σ(I): 24.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.91-1.943.70.3081100
1.94-1.963.70.2751100
1.96-1.993.70.2381100
1.99-2.023.70.2131100
2.02-2.063.70.195199.9
2.06-2.093.70.1721100
2.09-2.133.80.1531100
2.13-2.173.80.1371100
2.17-2.223.80.129199.9
2.22-2.263.80.1231100
2.26-2.323.80.1061100
2.32-2.373.80.0991100
2.37-2.443.80.091100
2.44-2.513.80.0851100
2.51-2.593.80.0771100
2.59-2.683.90.0681100
2.68-2.793.80.0611100
2.79-2.923.90.0591100
2.92-3.073.90.0521100
3.07-3.263.90.0461100
3.26-3.523.90.0391100
3.52-3.873.90.0361100
3.87-4.433.90.0311100
4.43-5.573.80.027199.9
5.57-253.70.026198.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.91→24.786 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 18.93
RfactorNum. reflection% reflection
Rfree0.1886 5151 4.98 %
Rwork0.1579 --
obs0.1595 103359 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.57 Å2 / Biso mean: 24.7207 Å2 / Biso min: 5.34 Å2
Refinement stepCycle: final / Resolution: 1.91→24.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8211 0 124 859 9194
Biso mean--31.68 32.54 -
Num. residues----1099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068651
X-RAY DIFFRACTIONf_angle_d0.811702
X-RAY DIFFRACTIONf_chiral_restr0.0511331
X-RAY DIFFRACTIONf_plane_restr0.0051550
X-RAY DIFFRACTIONf_dihedral_angle_d20.8543262
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.91-1.93170.31021700.251332593429100
1.9317-1.95440.26461600.231832723432100
1.9544-1.97830.2321910.210732733464100
1.9783-2.00330.25041820.190532523434100
2.0033-2.02960.21811840.184532783462100
2.0296-2.05740.18091560.179832923448100
2.0574-2.08680.22621640.188332793443100
2.0868-2.11790.25261820.186132593441100
2.1179-2.1510.22481570.177632913448100
2.151-2.18630.23871620.169533193481100
2.1863-2.22390.19541720.170732543426100
2.2239-2.26430.23521790.176532953474100
2.2643-2.30790.23051650.169732033368100
2.3079-2.35490.18541740.160333413515100
2.3549-2.40610.1891860.16132463432100
2.4061-2.4620.22791760.160532763452100
2.462-2.52350.19121640.1632603424100
2.5235-2.59170.21622030.166432853488100
2.5917-2.66790.22761560.163332783434100
2.6679-2.75390.17191760.153132683444100
2.7539-2.85220.19791700.157832973467100
2.8522-2.96620.21421680.162432793447100
2.9662-3.10090.18691550.166533023457100
3.1009-3.26410.1891810.161832513432100
3.2641-3.46810.18051470.150633073454100
3.4681-3.7350.16611850.140532743459100
3.735-4.10940.14741800.127432613441100
4.1094-4.70050.13561650.118432973462100
4.7005-5.90880.13751770.142832563433100
5.9088-24.78830.16651640.1493204336897

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