[English] 日本語
Yorodumi
- PDB-6e2y: MDDEF in complex with MVAPP, ADP, sulfate and cobalt. Anomalous data -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6e2y
TitleMDDEF in complex with MVAPP, ADP, sulfate and cobalt. Anomalous data
ComponentsMevalonate diphosphate decarboxylase
KeywordsLYASE / Mevalonate diphosphate decarboxylase
Function / homology
Function and homology information


diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / ATP binding / metal ion binding / 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
ADENOSINE-5'-DIPHOSPHATE / : / Chem-DP6 / diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsStauffacher, C.V. / Chen, C.-L.
CitationJournal: Nat Commun / Year: 2020
Title: Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase.
Authors: Chen, C.L. / Paul, L.N. / Mermoud, J.C. / Steussy, C.N. / Stauffacher, C.V.
History
DepositionJul 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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 diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2266
Polymers39,2761
Non-polymers9495
Water2,558142
1
A: Mevalonate diphosphate decarboxylase
hetero molecules

A: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,45112
Polymers78,5532
Non-polymers1,89810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area5480 Å2
ΔGint-157 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.878, 98.016, 45.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Mevalonate diphosphate decarboxylase / Diphosphomevalonate decarboxylase


Mass: 39276.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: mvaD, B6S42_02310 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9FD68, diphosphomevalonate decarboxylase

-
Non-polymers , 5 types, 147 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-DP6 / (3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID


Mass: 308.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O10P2
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Crystals were produced under the conditions of 1.6 M ammonium sulfate, 50 mM sodium acetate, pH 4.6; buffer exchange was performed under the conditions of 26 % PEG 3350, 5 mM CoCl2 and 50 mM ...Details: Crystals were produced under the conditions of 1.6 M ammonium sulfate, 50 mM sodium acetate, pH 4.6; buffer exchange was performed under the conditions of 26 % PEG 3350, 5 mM CoCl2 and 50 mM sodium acetate, pH 4.6; Crystals were soaked with MVAPP (200 micromole), followed by ATPgS (200 micromole). Then condensation was conducted at 30 % PEG 3350, 15% PEG 400, 5 mM CoCl2, 50 mM sodium acetate, pH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.34→30 Å / Num. obs: 15794 / % possible obs: 99.5 % / Redundancy: 12.7 % / Rpim(I) all: 0.022 / Net I/σ(I): 40
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1541 / CC1/2: 0.92 / Rpim(I) all: 0.144 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V2L

5v2l


Resolution: 2.34→26.612 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.18
RfactorNum. reflection% reflection
Rfree0.2254 1425 5.02 %
Rwork0.1871 --
obs0.1889 15594 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.34→26.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 52 142 2722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012631
X-RAY DIFFRACTIONf_angle_d1.0043569
X-RAY DIFFRACTIONf_dihedral_angle_d14.197938
X-RAY DIFFRACTIONf_chiral_restr0.053392
X-RAY DIFFRACTIONf_plane_restr0.006454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.42360.25871380.21322245X-RAY DIFFRACTION81
2.4236-2.52060.27231440.21032584X-RAY DIFFRACTION93
2.5206-2.63520.29741510.20822750X-RAY DIFFRACTION99
2.6352-2.7740.22031730.20172725X-RAY DIFFRACTION100
2.774-2.94760.22031240.20282801X-RAY DIFFRACTION100
2.9476-3.17480.26511590.21072787X-RAY DIFFRACTION100
3.1748-3.49370.19371150.20062812X-RAY DIFFRACTION100
3.4937-3.99780.20241520.17572751X-RAY DIFFRACTION99
3.9978-5.03120.2071360.16032722X-RAY DIFFRACTION97
5.0312-26.61370.21971330.1692771X-RAY DIFFRACTION99

+
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