[English] 日本語
Yorodumi
- PDB-7lnv: Apo Structure of Isopentenyl Phosphate Kinase from Candidatus met... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lnv
TitleApo Structure of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus
ComponentsIsopentenyl phosphate kinase
KeywordsTRANSFERASE / Phosphotransferase ATP Biocatalysis Isoprenoids Enzyme Promiscuity
Function / homology
Function and homology information


isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / terpenoid biosynthetic process / kinase activity / ATP binding / cytosol
Similarity search - Function
Fosfomycin resistance kinase, FomA-type / Glutamate/acetylglutamate kinase / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family
Similarity search - Domain/homology
MALONATE ION / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesCandidatus Methanomethylophilus alvus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsThomas, L.M. / Singh, S. / Scull, E.M. / Bourne, C.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus .
Authors: Johnson, B.P. / Kumar, V. / Scull, E.M. / Thomas, L.M. / Bourne, C.R. / Singh, S.
History
DepositionFeb 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isopentenyl phosphate kinase
B: Isopentenyl phosphate kinase
C: Isopentenyl phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9887
Polymers91,6003
Non-polymers3884
Water4,053225
1
B: Isopentenyl phosphate kinase
C: Isopentenyl phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3635
Polymers61,0662
Non-polymers2963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-21 kcal/mol
Surface area21830 Å2
MethodPISA
2
A: Isopentenyl phosphate kinase
hetero molecules

A: Isopentenyl phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2514
Polymers61,0662
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area3660 Å2
ΔGint-24 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.392, 45.630, 113.874
Angle α, β, γ (deg.)90.000, 121.200, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-466-

HOH

-
Components

#1: Protein Isopentenyl phosphate kinase / IPK


Mass: 30533.225 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Methanomethylophilus alvus (archaea)
Gene: BKD89_07040 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3G3II74, isopentenyl phosphate kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: 0.2 M Sodium Malonate pH 7.0, 20% PEG 3350.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 25, 2016 / Details: Osmic Veri Max mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 44070 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 29.89 Å2 / CC1/2: 0.997 / Χ2: 0.982 / Net I/σ(I): 9.91
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 2159 / CC1/2: 0.552

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-30001.17.1_3660data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LKK

3lkk


Resolution: 2.2→37.29 Å / SU ML: 0.3045 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1766
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2814 2005 4.55 %
Rwork0.2278 42048 -
obs0.2303 44053 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 0 26 225 5857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00295711
X-RAY DIFFRACTIONf_angle_d0.51977679
X-RAY DIFFRACTIONf_chiral_restr0.0437885
X-RAY DIFFRACTIONf_plane_restr0.0038997
X-RAY DIFFRACTIONf_dihedral_angle_d7.8516801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.34751360.32062880X-RAY DIFFRACTION97.57
2.25-2.310.33181430.2993003X-RAY DIFFRACTION99.59
2.31-2.380.30881410.28292961X-RAY DIFFRACTION99.49
2.38-2.460.33351360.27152965X-RAY DIFFRACTION99.97
2.46-2.550.30051470.26863017X-RAY DIFFRACTION99.97
2.55-2.650.32921370.26722975X-RAY DIFFRACTION100
2.65-2.770.33851470.26462986X-RAY DIFFRACTION99.97
2.77-2.910.32091350.26463010X-RAY DIFFRACTION100
2.91-3.10.32731470.24662982X-RAY DIFFRACTION100
3.1-3.340.24941500.22583023X-RAY DIFFRACTION100
3.34-3.670.26511450.21023015X-RAY DIFFRACTION100
3.67-4.20.25341370.19613039X-RAY DIFFRACTION99.87
4.2-5.290.22061530.18083039X-RAY DIFFRACTION99.87
5.29-37.290.28211510.19863153X-RAY DIFFRACTION99.7

+
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