[English] 日本語
Yorodumi
- PDB-3k4o: Crystal Structure of Isopentenyl Phosphate Kinase from Methanocal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k4o
TitleCrystal Structure of Isopentenyl Phosphate Kinase from Methanocaldococcus jannaschii
Componentsisopentenyl phosphate kinase
KeywordsTRANSFERASE / small molecule kinase / ATP-binding / Methanocaldococcus jannaschii / isopentenyl monophosphate / isopentenyl diphosphate / isoprenoid biosynthesis / mevalonate pathway / archaea
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 / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Isopentenyl phosphate kinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsDellas, N. / Noel, J.P.
CitationJournal: Acs Chem.Biol. / Year: 2010
Title: Mutation of archaeal isopentenyl phosphate kinase highlights mechanism and guides phosphorylation of additional isoprenoid monophosphates.
Authors: Dellas, N. / Noel, J.P.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: isopentenyl phosphate kinase
B: isopentenyl phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,09311
Polymers60,0192
Non-polymers1,0749
Water2,756153
1


  • Idetical with deposited unit in distinct coordinate
  • defined by author&software
TypeNameSymmetry operationNumber
crystal symmetry operation2_655-x+1,-y,z1
Buried area5150 Å2
ΔGint-173 kcal/mol
Surface area21850 Å2
MethodPISA
2
A: isopentenyl phosphate kinase
B: isopentenyl phosphate kinase
hetero molecules

A: isopentenyl phosphate kinase
B: isopentenyl phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,18622
Polymers120,0394
Non-polymers2,14718
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_655-x+1,-y,z1
identity operation1_555x,y,z1
Buried area13390 Å2
ΔGint-368 kcal/mol
Surface area40610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.200, 99.700, 87.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-315-

HOH

21A-341-

HOH

-
Components

#1: Protein isopentenyl phosphate kinase


Mass: 30009.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0044 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60352
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.6M ammonium sulfate, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2008
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 45927 / Num. obs: 45753 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.36 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.54
Reflection shellResolution: 2→2.12 Å / Redundancy: 6.36 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 4.07 / Num. unique all: 7299 / % possible all: 98.3

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVE2.11phasing
CNSrefinement
PDB_EXTRACT3.005data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.05→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.831 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.241 2105 4.9 %
Rwork0.223 --
obs-42577 99.9 %
Solvent computationBsol: 64.48 Å2
Displacement parametersBiso max: 103.64 Å2 / Biso mean: 41.29 Å2 / Biso min: 17.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.407 Å20 Å20 Å2
2--1.84 Å20 Å2
3----3.247 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4079 0 37 153 4269
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5741.5
X-RAY DIFFRACTIONc_scbond_it2.0952
X-RAY DIFFRACTIONc_mcangle_it2.5622
X-RAY DIFFRACTIONc_scangle_it3.1842.5
X-RAY DIFFRACTIONc_angle_deg1.21282
X-RAY DIFFRACTIONc_bond_d0.005547
LS refinement shellResolution: 2.05→2.07 Å
RfactorNum. reflection
Rfree0.3236 47
Rwork0.2864 -
obs-927
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

+
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