[English] 日本語
Yorodumi
- PDB-2r3v: The Biochemical and Structural Basis for Feedback Inhibition of M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r3v
TitleThe Biochemical and Structural Basis for Feedback Inhibition of Mevalonate Kinase and Isoprenoid Metabolism
ComponentsMevalonate kinase
KeywordsTRANSFERASE / Mevalonate Kinase / Farnesyl thiodiphophate / ATP-binding / Cataract / Cholesterol biosynthesis / Cytoplasm / Disease mutation / Lipid synthesis / Nucleotide-binding / Peroxisome / Polymorphism / Steroid biosynthesis / Sterol biosynthesis
Function / homology
Function and homology information


mevalonate kinase / mevalonate kinase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / Cholesterol biosynthesis / isoprenoid biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / negative regulation of inflammatory response / peroxisome / intracellular membrane-bounded organelle ...mevalonate kinase / mevalonate kinase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / Cholesterol biosynthesis / isoprenoid biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / negative regulation of inflammatory response / peroxisome / intracellular membrane-bounded organelle / magnesium ion binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Mevalonate kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 ...Mevalonate kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFu, Z. / Voynova, N.E. / Miziorko, H.M. / Kim, J.P.
CitationJournal: Biochemistry / Year: 2008
Title: Biochemical and Structural Basis for Feedback Inhibition of Mevalonate Kinase and Isoprenoid Metabolism.
Authors: Fu, Z. / Voynova, N.E. / Herdendorf, T.J. / Miziorko, H.M. / Kim, J.J.
History
DepositionAug 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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: Mevalonate kinase
B: Mevalonate kinase
C: Mevalonate kinase
D: Mevalonate kinase


Theoretical massNumber of molelcules
Total (without water)169,9914
Polymers169,9914
Non-polymers00
Water4,053225
1
A: Mevalonate kinase


Theoretical massNumber of molelcules
Total (without water)42,4981
Polymers42,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mevalonate kinase


Theoretical massNumber of molelcules
Total (without water)42,4981
Polymers42,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mevalonate kinase


Theoretical massNumber of molelcules
Total (without water)42,4981
Polymers42,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mevalonate kinase


Theoretical massNumber of molelcules
Total (without water)42,4981
Polymers42,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Mevalonate kinase
B: Mevalonate kinase


Theoretical massNumber of molelcules
Total (without water)84,9962
Polymers84,9962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33150 Å2
MethodPISA
6
C: Mevalonate kinase
D: Mevalonate kinase


Theoretical massNumber of molelcules
Total (without water)84,9962
Polymers84,9962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.030, 78.200, 109.450
Angle α, β, γ (deg.)90.00, 113.33, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Mevalonate kinase / MK


Mass: 42497.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MVK / Plasmid: pET-3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 DE3 / References: UniProt: Q03426, mevalonate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: MES buffer, PEG5k MME, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 25, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→29.37 Å / Num. obs: 46347 / % possible obs: 84.1 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 41.1 Å2 / Rsym value: 0.049 / Net I/σ(I): 17.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.18 / % possible all: 44.3

-
Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1kvk

1kvk


Resolution: 2.5→29.37 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 404877.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.282 3916 8.5 %RANDOM
Rwork0.239 ---
obs0.239 46301 84.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.6162 Å2 / ksol: 0.269456 e/Å3
Displacement parametersBiso mean: 48.4 Å2
Baniso -1Baniso -2Baniso -3
1--14.52 Å20 Å2-5.55 Å2
2--27.2 Å20 Å2
3----12.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11710 0 0 225 11935
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.356 197 8.2 %
Rwork0.372 2216 -
obs--44.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

+
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