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- PDB-5lnw: Crystal structure of Arabidopsis thaliana Pdx1-I320-G3P complex -

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Basic information

Entry
Database: PDB / ID: 5lnw
TitleCrystal structure of Arabidopsis thaliana Pdx1-I320-G3P complex
ComponentsPyridoxal 5'-phosphate synthase subunit PDX1.3
KeywordsLYASE / beta/alpha barrel / pyridoxal phosphate synthase / glutamine amidotransferase / vitamin B6 biosythesis
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
Chem-HG3 / Chem-K8P / 5-O-phosphono-beta-D-ribofuranose / Pyridoxal 5'-phosphate synthase subunit PDX1.3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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 FoundationTE 368 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 2.0May 22, 2019Group: Atomic model / Data collection / Refinement description
Category: atom_site / diffrn_radiation_wavelength / refine_analyze
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Oct 23, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)139,79518
Polymers136,8614
Non-polymers2,93414
Water9,296516
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)419,38554
Polymers410,58412
Non-polymers8,80142
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 area46710 Å2
ΔGint-115 kcal/mol
Surface area97880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.261, 178.261, 115.309
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
11(chain A and resseq 500)
21(chain B and resseq 500)
31(chain C and resseq 500)
41(chain D and resseq 500)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resseq 500)A500
211(chain B and resseq 500)B500
311(chain C and resseq 500)C500
411(chain D and resseq 500)D500

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#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 BL21(DE3) (bacteria)
References: UniProt: Q8L940, pyridoxal 5'-phosphate synthase (glutamine hydrolysing)
#3: Sugar
ChemComp-RP5 / 5-O-phosphono-beta-D-ribofuranose / [(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE


Type: D-saccharide, beta linking / Mass: 230.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H11O8P
IdentifierTypeProgram
b-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 526 molecules

#2: Chemical
ChemComp-K8P / [(2~{R},3~{R})-2,3-bis(oxidanyl)-3-[[(2~{S})-3-oxidanylidenepent-4-en-2-yl]amino]propyl] dihydrogen phosphate


Mass: 269.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H16NO7P
#4: Chemical
ChemComp-HG3 / [(2~{R})-2,3,3-tris(oxidanyl)propyl] dihydrogen phosphate


Mass: 188.073 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9O7P
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.65 Å3/Da / Density % sol: 53.59 % / Mosaicity: 0.12 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH8.5, 0.2 M sodium acetate pH5.5, 10%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97525 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97525 Å / Relative weight: 1
ReflectionResolution: 1.9→44.57 Å / Num. obs: 107077 / % possible obs: 99.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 26.59 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.074 / Rrim(I) all: 0.145 / Net I/σ(I): 6.1 / Num. measured all: 345059 / Scaling rejects: 243
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.9330.8611592952400.4470.5851.0471.397.8
10.41-44.573.30.14420746240.9460.0830.16813.295.2

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
Aimless0.5.15data scaling
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→44.565 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 5461 5.1 %
Rwork0.1807 101586 -
obs0.1826 107047 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96 Å2 / Biso mean: 34.629 Å2 / Biso min: 12.57 Å2
Refinement stepCycle: final / Resolution: 1.9→44.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8054 0 180 516 8750
Biso mean--45.36 35.32 -
Num. residues----1074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068462
X-RAY DIFFRACTIONf_angle_d0.93411441
X-RAY DIFFRACTIONf_chiral_restr0.0751320
X-RAY DIFFRACTIONf_plane_restr0.0051497
X-RAY DIFFRACTIONf_dihedral_angle_d22.8753202
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A17X-RAY DIFFRACTIONPOSITIONAL0.023
12B17X-RAY DIFFRACTIONPOSITIONAL0.023
13C17X-RAY DIFFRACTIONPOSITIONAL0.023
14D17X-RAY DIFFRACTIONPOSITIONAL0.028
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 (%)
1.9-1.92160.40361800.35723320350097
1.9216-1.94420.35731940.336933853579100
1.9442-1.96790.33271860.306234043590100
1.9679-1.99280.35361560.301234673623100
1.9928-2.0190.30521870.287833553542100
2.019-2.04670.30382030.276533963599100
2.0467-2.07590.2921840.268234103594100
2.0759-2.10690.31432120.251633613573100
2.1069-2.13990.29431740.237134233597100
2.1399-2.17490.2991660.241934313597100
2.1749-2.21240.28521860.2333823568100
2.2124-2.25270.26861880.215234313619100
2.2527-2.2960.25571630.208833913554100
2.296-2.34290.24851800.202134053585100
2.3429-2.39380.24171690.193934063575100
2.3938-2.44950.23821600.185534393599100
2.4495-2.51070.23292090.179333693578100
2.5107-2.57860.22351630.179233983561100
2.5786-2.65450.21471920.175233723564100
2.6545-2.74010.19721830.16534193602100
2.7401-2.83810.2221550.16713427358299
2.8381-2.95170.23381540.17773401355599
2.9517-3.0860.23222320.17683349358199
3.086-3.24860.23392140.16763345355999
3.2486-3.45210.1842110.15653326353799
3.4521-3.71850.19111360.14863427356399
3.7185-4.09250.15391430.13363418356199
4.0925-4.68410.13371550.12093369352499
4.6841-5.89930.18252480.14723270351898
5.8993-44.57750.17891780.16423290346897
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)
11.71751.003-0.0242.402-0.64281.00530.0725-0.3404-0.06030.4421-0.1012-0.1522-0.08030.00510.0240.24740.0127-0.05830.20820.05650.214422.5995-33.1081-10.5454
21.5895-0.0028-0.81050.7345-0.85632.1173-0.0412-0.1407-0.20590.15240.01640.0294-0.0163-0.04880.02690.17740.00650.00790.10360.03460.22928.1503-37.6806-20.5895
32.6205-0.499-0.26640.8933-0.35741.2424-0.1384-0.4442-0.24250.27490.13950.1398-0.0366-0.0421-0.01820.28240.03070.05750.19860.10210.2858-17.4167-36.2383-10.7509
41.2252-0.4748-0.69791.23040.19851.2585-0.0611-0.1547-0.18810.23030.05190.2199-0.0028-0.06960.03030.15110.00250.05820.16490.04550.2673-28.6139-25.9746-20.6897
51.1806-0.9143-0.06371.2850.92991.88720.10030.4816-0.3832-0.3548-0.08390.1177-0.01050.0491-0.00380.3035-0.0171-0.05160.4049-0.16590.3052-17.7385-35.9646-65.8079
61.40340.015-0.58480.67460.21461.6078-0.01870.3377-0.3428-0.1877-0.0111-0.01710.1240.01360.07840.20690.0237-0.00060.2412-0.13080.2929-2.8984-38.896-55.0154
71.22110.64790.19590.67470.01880.6492-0.09610.5718-0.4224-0.49950.0105-0.3365-0.1363-0.1481-0.02660.43540.07410.11570.4215-0.12560.157122.5606-33.2994-65.9192
80.83090.4459-0.54631.2001-0.38621.30540.01980.2237-0.0587-0.2964-0.0301-0.2332-0.0694-0.02440.04040.22330.04980.09540.2258-0.02460.229532.3034-22.1851-54.6705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 22:143)A22 - 143
2X-RAY DIFFRACTION2(chain A and resid 144:295)A144 - 295
3X-RAY DIFFRACTION3(chain B and resid 21:144)B21 - 144
4X-RAY DIFFRACTION4(chain B and resid 145:292)B145 - 292
5X-RAY DIFFRACTION5(chain C and resid 22:143)C22 - 143
6X-RAY DIFFRACTION6(chain C and resid 144:291)C144 - 291
7X-RAY DIFFRACTION7(chain D and resid 23:143)D23 - 143
8X-RAY DIFFRACTION8(chain D and resid 144:288)D144 - 291

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