[English] 日本語
Yorodumi
- PDB-7e4l: Conversion of pyrophosphate-dependent myo-inositol-1 kinase into ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e4l
TitleConversion of pyrophosphate-dependent myo-inositol-1 kinase into myo-inositol-3 kinase by N78L/S89L mutation
ComponentsPfkB domain-containing protein
KeywordsTRANSFERASE / pyrophosphate-dependent kinase
Function / homologyPPi-dependent kinase / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like / METHYLENEDIPHOSPHONIC ACID / PfkB domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsTashiro, R. / Miki, K. / Fujihashi, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Altering the Phosphorylation Position of Pyrophosphate-Dependent myo -Inositol-1-Kinase Based on Its Crystal Structure.
Authors: Tashiro, R. / Sato, T. / Atomi, H. / Miki, K. / Fujihashi, M.
History
DepositionFeb 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PfkB domain-containing protein
B: PfkB domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6606
Polymers64,2602
Non-polymers4014
Water3,477193
1
A: PfkB domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3303
Polymers32,1301
Non-polymers2002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-5 kcal/mol
Surface area11690 Å2
MethodPISA
2
B: PfkB domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3303
Polymers32,1301
Non-polymers2002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-5 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.205, 46.398, 66.544
Angle α, β, γ (deg.)83.53, 80.43, 68.57
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein PfkB domain-containing protein / pyrophosphate-dependent myo-inositol-1 kinase


Mass: 32129.789 Da / Num. of mol.: 2 / Mutation: N78L/S89L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: Tmari_0412 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: R4NYE9
#2: Chemical ChemComp-MDN / METHYLENEDIPHOSPHONIC ACID / Medronic acid


Mass: 176.002 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH6O6P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 26% (w/v) poly(ethylene glycol) 4000, 2mM ammonium sulfate, 100mM sodium acetate buffer (pH 5.4)

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 43707 / % possible obs: 62.5 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rrim(I) all: 0.051 / Net I/σ(I): 19.8
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.58 % / Mean I/σ(I) obs: 9.1 / Num. unique obs: 4684 / CC1/2: 0.985 / Rrim(I) all: 0.134 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5ysp
Resolution: 1.6→42.65 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21555 2173 5 %RANDOM
Rwork0.19179 ---
obs0.19301 41534 65.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.558 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20.21 Å20.15 Å2
2---0.33 Å20.32 Å2
3---0.87 Å2
Refinement stepCycle: 1 / Resolution: 1.6→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4266 0 20 193 4479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134399
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174176
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.6425958
X-RAY DIFFRACTIONr_angle_other_deg2.3071.5789582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8645559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.02420.952210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65815728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.991531
X-RAY DIFFRACTIONr_chiral_restr0.0570.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024939
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021027
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8941.6072233
X-RAY DIFFRACTIONr_mcbond_other0.8931.6062232
X-RAY DIFFRACTIONr_mcangle_it1.5132.4072790
X-RAY DIFFRACTIONr_mcangle_other1.5132.4072791
X-RAY DIFFRACTIONr_scbond_it1.0471.7232166
X-RAY DIFFRACTIONr_scbond_other1.0481.7242164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6892.5373168
X-RAY DIFFRACTIONr_long_range_B_refined3.23318.5684755
X-RAY DIFFRACTIONr_long_range_B_other3.21818.5274744
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 218 -
Rwork0.218 4459 -
obs--94.47 %

+
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