[English] 日本語
Yorodumi
- PDB-5iiq: Structure of the SPX-TTM domain fragment of the yeast inorganic p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iiq
TitleStructure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form B).
ComponentsVacuolar transporter chaperone 4
KeywordsTRANSFERASE / helical bundle / alpha-helical hairpin / inositol phosphate binding / protein-protein interaction / chaperone
Function / homology
Function and homology information


vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / vacuole fusion, non-autophagic / microautophagy / polyphosphate metabolic process / vacuolar transport / inositol hexakisphosphate binding ...vacuolar transporter chaperone complex / ATP-polyphosphate phosphotransferase / polyphosphate biosynthetic process / engulfment of target by autophagosome / polyphosphate kinase activity / vacuole fusion, non-autophagic / microautophagy / polyphosphate metabolic process / vacuolar transport / inositol hexakisphosphate binding / fungal-type vacuole membrane / vacuolar membrane / autophagosome membrane / cell periphery / cell cortex / cytoplasmic vesicle / calmodulin binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
VTC, catalytic tunnel domain / VTC domain superfamily / Domain of unknown function DUF202 / VTC domain / Domain of unknown function (DUF202) / VTC domain / mRNA Triphosphatase Cet1; Chain A / SPX domain / SPX domain profile. / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE 2- / Vacuolar transporter chaperone complex subunit 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsWild, R. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Reseacrh Council310856 Switzerland
CitationJournal: Science / Year: 2016
Title: Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains.
Authors: Wild, R. / Gerasimaite, R. / Jung, J.Y. / Truffault, V. / Pavlovic, I. / Schmidt, A. / Saiardi, A. / Jessen, H.J. / Poirier, Y. / Hothorn, M. / Mayer, A.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vacuolar transporter chaperone 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4165
Polymers56,9521
Non-polymers4644
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-44 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.041, 92.041, 301.732
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein Vacuolar transporter chaperone 4 / Phosphate metabolism protein 3


Mass: 56951.621 Da / Num. of mol.: 1 / Fragment: SPX domain- TTM domain, UNP residues 2-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VTC4, PHM3, YJL012C, J1345 / Plasmid: pMH-HT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P47075
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 1.5M AmSO4, 4% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 3.03→50 Å / Num. obs: 15492 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 20.7 % / Biso Wilson estimate: 99.42 Å2 / CC1/2: 1 / Rsym value: 0.108 / Net I/σ(I): 28.4
Reflection shellResolution: 3.03→3.21 Å / Redundancy: 18.3 % / Mean I/σ(I) obs: 2.99 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3g3r

3g3r


Resolution: 3.03→19.88 Å / Cor.coef. Fo:Fc: 0.9234 / Cor.coef. Fo:Fc free: 0.9174 / SU R Cruickshank DPI: 3.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.395 / SU Rfree Cruickshank DPI: 0.395
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 774 5 %RANDOM
Rwork0.2246 ---
obs0.2266 15479 99.74 %-
Displacement parametersBiso mean: 94.81 Å2
Baniso -1Baniso -2Baniso -3
1--6.0116 Å20 Å20 Å2
2---6.0116 Å20 Å2
3---12.0232 Å2
Refine analyzeLuzzati coordinate error obs: 0.766 Å
Refinement stepCycle: 1 / Resolution: 3.03→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 24 0 3823
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083902HARMONIC2
X-RAY DIFFRACTIONt_angle_deg15280HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1388SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes110HARMONIC2
X-RAY DIFFRACTIONt_gen_planes552HARMONIC5
X-RAY DIFFRACTIONt_it3902HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.21
X-RAY DIFFRACTIONt_other_torsion19.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion494SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4266SEMIHARMONIC4
LS refinement shellResolution: 3.03→3.24 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.37 134 4.98 %
Rwork0.2665 2558 -
all0.2716 2692 -
obs--99.74 %
Refinement TLS params.Method: refined / Origin x: 38.0344 Å / Origin y: 35.3267 Å / Origin z: 302.91 Å
111213212223313233
T-0.4124 Å2-0.0235 Å20.0716 Å2-0.2787 Å2-0.0261 Å2--0.0351 Å2
L0.0418 °2-0.0379 °20.4371 °2-0.3585 °20.0397 °2--2.6246 °2
S-0.072 Å °-0.0221 Å °0.012 Å °-0.0107 Å °0.2223 Å °0.1549 Å °0.1636 Å °-0.2283 Å °-0.1504 Å °
Refinement TLS groupSelection details: { A|* }

+
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