[English] 日本語
Yorodumi
- PDB-5lnv: Crystal structure of Arabidopsis thaliana Pdx1-I320 complex from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lnv
TitleCrystal structure of Arabidopsis thaliana Pdx1-I320 complex from multiple crystals
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 / 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
(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: 2.24 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
Revision 1.3Sep 19, 2018Group: Data collection / Database references
Category: citation_author / diffrn ...citation_author / diffrn / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source
Item: _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water10,323573
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
Unit cell
Length a, b, c (Å)178.576, 178.576, 117.375
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 98 or resseq 166 or resseq 500))
21(chain B and (resseq 98 or resseq 166 or resseq 500))
31(chain C and (resseq 98 or resseq 166 or resseq 500))
41(chain D and (resseq 98 or resseq 166 or resseq 500))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 98 or resseq 166 or resseq 500))A98
121(chain A and (resseq 98 or resseq 166 or resseq 500))A166
131(chain A and (resseq 98 or resseq 166 or resseq 500))A500
211(chain B and (resseq 98 or resseq 166 or resseq 500))B98
221(chain B and (resseq 98 or resseq 166 or resseq 500))B166
231(chain B and (resseq 98 or resseq 166 or resseq 500))B500
311(chain C and (resseq 98 or resseq 166 or resseq 500))C98
321(chain C and (resseq 98 or resseq 166 or resseq 500))C166
331(chain C and (resseq 98 or resseq 166 or resseq 500))C500
411(chain D and (resseq 98 or resseq 166 or resseq 500))D98
421(chain D and (resseq 98 or resseq 166 or resseq 500))D166
431(chain D and (resseq 98 or resseq 166 or resseq 500))D500

-
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 / Phosphate


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


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 / Water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.57 % / Mosaicity: 0.12 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M Tris pH7,1-8.5, 0.4 M sodium acetate pH5.5, 4.8-11.85%(w/v) PEG4000

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.976253
SYNCHROTRONESRF ID23-130.976253
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELDec 15, 2013
DECTRIS PILATUS3 6M3PIXELDec 16, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.9762531
30.9762531
ReflectionResolution: 2.24→46.75 Å / Num. obs: 66626 / % possible obs: 99.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 26.38 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.115 / Rrim(I) all: 0.246 / Net I/σ(I): 30.5 / Num. measured all: 284330 / Scaling rejects: 1710
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.24-2.294.21.3610.426199.2
10.51-46.754.50.0810.991196.7

-
Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.24→46.748 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 23.94
RfactorNum. reflection% reflection
Rfree0.2199 3294 5.06 %
Rwork0.1774 --
obs0.1795 65127 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.99 Å2 / Biso mean: 30.059 Å2 / Biso min: 10.26 Å2
Refinement stepCycle: final / Resolution: 2.24→46.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8289 0 68 573 8930
Biso mean--36.75 31.43 -
Num. residues----1106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118473
X-RAY DIFFRACTIONf_angle_d1.35511435
X-RAY DIFFRACTIONf_chiral_restr0.0841309
X-RAY DIFFRACTIONf_plane_restr0.0071516
X-RAY DIFFRACTIONf_dihedral_angle_d16.8115168
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A25X-RAY DIFFRACTIONPOSITIONAL0.016
12B25X-RAY DIFFRACTIONPOSITIONAL0.016
13C25X-RAY DIFFRACTIONPOSITIONAL0.016
14D25X-RAY DIFFRACTIONPOSITIONAL0.014
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.24-2.2720.34421370.30682479261694
2.272-2.3060.34731170.27912502261993
2.306-2.3420.29391300.26212520265095
2.342-2.38040.28691480.2472500264895
2.3804-2.42140.30521470.24262496264395
2.4214-2.46550.28921440.22322541268596
2.4655-2.51290.25741480.222530267896
2.5129-2.56420.24911440.20772559270396
2.5642-2.61990.31791270.21132558268596
2.6199-2.68080.24411080.19782599270797
2.6808-2.74790.23431460.18372565271197
2.7479-2.82220.27281290.18452566269597
2.8222-2.90520.25121490.19052559270898
2.9052-2.9990.22531320.19522606273898
2.999-3.10610.23141410.1742596273798
3.1061-3.23050.23511190.18042666278599
3.2305-3.37740.21071640.1642578274299
3.3774-3.55550.23351360.17082672280899
3.5555-3.77810.17211280.15632602273099
3.7781-4.06970.20931450.14582646279199
4.0697-4.47890.17061220.1362635275799
4.4789-5.12630.15181420.13422631277399
5.1263-6.4560.16391450.16372635278099
6.456-46.75810.16241460.14282592273898

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more