[English] 日本語
Yorodumi
- PDB-1fi4: THE X-RAY CRYSTAL STRUCTURE OF MEVALONATE 5-DIPHOSPHATE DECARBOXY... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fi4
TitleTHE X-RAY CRYSTAL STRUCTURE OF MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE AT 2.3 ANGSTROM RESOLUTION.
ComponentsMEVALONATE 5-DIPHOSPHATE DECARBOXYLASE
KeywordsLYASE / mixed alpha/beta structure / ATP binding / decarboxylase / cholesterol biosynthesis / structural genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Synthesis of dolichyl-phosphate / Cholesterol biosynthesis / diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / ergosterol biosynthetic process / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol biosynthetic process / vacuole / ATP binding / cytoplasm / cytosol
Similarity search - Function
Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / : / Diphosphomevalonate decarboxylase-like N-terminal domain / GHMP kinase, C-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 ...Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / : / Diphosphomevalonate decarboxylase-like N-terminal domain / GHMP kinase, C-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
Diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.27 Å
AuthorsBonanno, J.B. / Edo, C. / Eswar, N. / Pieper, U. / Romanowski, M.J. / Ilyin, V. / Gerchman, S.E. / Kycia, H. / Studier, F.W. / Sali, A. ...Bonanno, J.B. / Edo, C. / Eswar, N. / Pieper, U. / Romanowski, M.J. / Ilyin, V. / Gerchman, S.E. / Kycia, H. / Studier, F.W. / Sali, A. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis.
Authors: Bonanno, J.B. / Edo, C. / Eswar, N. / Pieper, U. / Romanowski, M.J. / Ilyin, V. / Gerchman, S.E. / Kycia, H. / Studier, F.W. / Sali, A. / Burley, S.K.
History
DepositionAug 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.6Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)46,8041
Polymers46,8041
Non-polymers00
Water2,954164
1
A: MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE

A: MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)93,6082
Polymers93,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2750 Å2
ΔGint-18 kcal/mol
Surface area31860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.796, 126.402, 47.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsphysiological dimer observed in crystal

-
Components

#1: Protein MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE / MDD / DIPHOSPHOMEVALONATE DECARBOXYLASE


Mass: 46804.043 Da / Num. of mol.: 1
Mutation: M1(MSE), M89(MSE), M169(MSE), M179(MSE), M192(MSE), M212(MSE), M237(MSE), M254(MSE), M255(MSE), M274(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: HIS-TAG MODIFIED PET28A PLASMID / Production host: Escherichia coli (E. coli)
References: UniProt: P32377, diphosphomevalonate decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl pH 8.5, 15% PEG 4K, 1M NaCl, 5% glycerol, 5% ethylene glycol, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris-HCl1reservoir
215 %(w/v)PEG40001reservoir
31 M1reservoirNaCl
45 %(v/v)ethylene glycol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 13, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 41954 / Num. obs: 40942 / % possible obs: 97.6 % / Observed criterion σ(F): 9999 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 25
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.227 / Num. unique all: 4206 / % possible all: 90.8
Reflection
*PLUS
Lowest resolution: 18 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 90.3 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
CNS0.9refinement
RefinementResolution: 2.27→30 Å / σ(F): 9999 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The model was refined against a target of maximum likelihood on solvent flattened phases except for the last round of Powell minimization when a target of maximum likelihood on F was used. ...Details: The model was refined against a target of maximum likelihood on solvent flattened phases except for the last round of Powell minimization when a target of maximum likelihood on F was used. The data were corrected for anomalous scattering by the selenium atoms.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 4094 -Random
Rwork0.239 ---
all0.242 41454 --
obs0.242 41454 100 %-
Refinement stepCycle: LAST / Resolution: 2.27→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 0 164 3226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.683
X-RAY DIFFRACTIONc_bond_d0.0077
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 18 Å / σ(F): 9999 / Rfactor obs: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3

+
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