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

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Basic information

Entry
Database: PDB / ID: 5lnu
TitleCrystal structure of Arabidopsis thaliana Pdx1-I320 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
(4~{S})-4-azanyl-5-oxidanyl-pent-1-en-3-one / PHOSPHATE ION / Pyridoxal 5'-phosphate synthase subunit PDX1.3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.73 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 United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light SourceFunding for PhD of M. Rodrigues United Kingdom
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

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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)138,08616
Polymers136,8614
Non-polymers1,22512
Water18,6821037
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)414,25848
Polymers410,58412
Non-polymers3,67436
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 area46770 Å2
ΔGint-466 kcal/mol
Surface area101750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.117, 178.117, 115.963
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: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-KIK / (4~{S})-4-azanyl-5-oxidanyl-pent-1-en-3-one


Mass: 115.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1037 / 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: 2.66 Å3/Da / Density % sol: 53.78 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH8.5, 0.13 M sodium acetate pH5.5, 12.25%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.73→52.2 Å / Num. obs: 141425 / % possible obs: 98.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 18.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.037 / Rrim(I) all: 0.066 / Net I/σ(I): 9.3 / Num. measured all: 408071 / Scaling rejects: 240
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
1.73-1.762.90.4452078971320.8410.3160.5481.999.7
9.48-52.23.20.02128218770.9990.0130.02529.999.4

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.73→46.346 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.91
RfactorNum. reflection% reflection
Rfree0.1912 7069 5.01 %
Rwork0.1624 --
obs0.1638 141161 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.18 Å2 / Biso mean: 24.1782 Å2 / Biso min: 8.37 Å2
Refinement stepCycle: final / Resolution: 1.73→46.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8289 0 68 1037 9394
Biso mean--30.33 33.81 -
Num. residues----1106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068538
X-RAY DIFFRACTIONf_angle_d0.81311535
X-RAY DIFFRACTIONf_chiral_restr0.0731318
X-RAY DIFFRACTIONf_plane_restr0.0051534
X-RAY DIFFRACTIONf_dihedral_angle_d21.1943194
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 (%)
1.73-1.74970.32612260.288445514777100
1.7497-1.77030.32300.280345514781100
1.7703-1.79180.28992240.279545044728100
1.7918-1.81450.31232440.262345224766100
1.8145-1.83840.27832340.252745644798100
1.8384-1.86360.27282450.24145274772100
1.8636-1.89020.28092330.232344694702100
1.8902-1.91840.25472590.22584500475999
1.9184-1.94840.25542320.21224490472299
1.9484-1.98040.25262290.2034512474199
1.9804-2.01450.24382470.19584442468999
2.0145-2.05110.2332240.19184481470598
2.0511-2.09060.23542230.18674436465998
2.0906-2.13330.21622150.18084410462596
2.1333-2.17960.20832140.17424256447094
2.1796-2.23030.20922450.164155440092
2.2303-2.28610.20432350.15894451468697
2.2861-2.34790.18932410.152644824723100
2.3479-2.4170.19122610.153345424803100
2.417-2.4950.18782510.15144824733100
2.495-2.58420.1942530.146445564809100
2.5842-2.68770.18682100.146445574767100
2.6877-2.810.16082390.138545194758100
2.81-2.95810.17012470.146645384785100
2.9581-3.14340.18482320.14745384770100
3.1434-3.3860.17842560.145544634719100
3.386-3.72660.14942310.13554508473999
3.7266-4.26550.1471990.12374098429790
4.2655-5.37290.1292350.12714470470599
5.3729-46.36250.16632550.151545184773100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.98990.2051-0.20440.9297-0.1190.30260.0275-0.1921-0.0880.1738-0.0349-0.0533-0.01870.02980.01070.17020.0017-0.03620.14650.02930.144322.3963-32.8653-10.3939
20.70960.0397-0.08520.2016-0.08252.04770.03260.0388-0.08760.0339-0.0216-0.01460.0504-0.0049-0.02030.1090.0051-0.00430.06670.01720.130813.4691-35.6848-29.2678
32.53760.07850.01242.9736-0.17412.2794-0.0064-0.2469-0.00350.31960.06050.1759-0.1151-0.1023-0.04260.15670.03830.01180.12830.0560.15692.6119-39.0671-8.2565
41.3595-0.2535-0.03111.23710.01090.5934-0.0821-0.2654-0.13050.24350.10650.16050.0603-0.0522-0.02090.17460.02610.03480.14760.06860.1794-17.3881-35.7259-10.4415
50.6592-0.21190.00360.36220.01591.1494-0.0249-0.0264-0.12510.01250.00760.09710.0218-0.04710.00290.0908-0.00420.01140.09860.01740.1611-23.8263-30.0147-29.0418
63.4684-0.69120.41981.90830.46883.08170.0026-0.3483-0.01250.2620.07630.1533-0.1061-0.0195-0.06330.18410.00830.08250.14180.05510.1903-32.3849-21.933-8.3803
71.5067-0.46410.06611.08390.2660.89180.07610.3913-0.224-0.2323-0.05260.05220.05850.0041-0.01270.1706-0.0006-0.03370.246-0.09130.1893-16.9749-35.8611-66.7194
80.8863-0.1206-0.17580.3768-0.28941.33070.02950.1313-0.1236-0.0467-0.03550.00580.01880.0423-0.00550.10650.0089-0.00320.1076-0.0470.151-7.839-35.6671-48.9831
92.1854-0.028-1.65131.00640.45994.14170.03850.3617-0.163-0.22070.0434-0.0851-0.0448-0.0058-0.0380.14980.0108-0.0280.1797-0.08960.20490.0492-40.0751-63.0601
101.62750.5132-0.0361.09350.00450.5324-0.09880.3646-0.1062-0.29830.0701-0.0841-0.0404-0.04970.03120.20860.02330.0350.2159-0.05790.147522.2712-32.6853-66.6643
110.49960.3905-0.10110.6179-0.32381.6616-0.00840.1013-0.0571-0.0538-0.0039-0.043-0.0744-0.01120.00230.08910.03390.03070.1074-0.01980.145527.2979-23.9641-48.8265
121.34950.546-1.17151.4656-0.96783.08230.0420.28280.0574-0.27330.0704-0.1033-0.0583-0.174-0.07050.17780.03860.04990.1601-0.04090.191934.6453-20.0772-62.7114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 22:138)A22 - 138
2X-RAY DIFFRACTION2(chain A and resid 139:226)A139 - 226
3X-RAY DIFFRACTION3(chain A and resid 227:298)A227 - 298
4X-RAY DIFFRACTION4(chain B and resid 21:136)B21 - 136
5X-RAY DIFFRACTION5(chain B and resid 137:225)B137 - 225
6X-RAY DIFFRACTION6(chain B and resid 226:298)B226 - 298
7X-RAY DIFFRACTION7(chain C and resid 22:136)C22 - 136
8X-RAY DIFFRACTION8(chain C and resid 137:206)C137 - 206
9X-RAY DIFFRACTION9(chain C and resid 207:297)C207 - 297
10X-RAY DIFFRACTION10(chain D and resid 23:138)D23 - 138
11X-RAY DIFFRACTION11(chain D and resid 139:205)D139 - 205
12X-RAY DIFFRACTION12(chain D and resid 206:297)D206 - 297

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