[English] 日本語
Yorodumi
- PDB-6fmv: IMISX-EP of Hg-BacA soaking SIRAS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fmv
TitleIMISX-EP of Hg-BacA soaking SIRAS
ComponentsUndecaprenyl-diphosphatase
KeywordsHYDROLASE / Serial crystallography / experimental phasing / in meso crystallization / in situ diffraction data collection / membrane protein structure.
Function / homology
Function and homology information


undecaprenyl-diphosphate phosphatase / undecaprenyl-diphosphatase activity / pyrophosphatase activity / dephosphorylation / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / plasma membrane
Similarity search - Function
Undecaprenyl-diphosphatase UppP / Bacitracin resistance protein BacA
Similarity search - Domain/homology
CITRATE ANION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Undecaprenyl-diphosphatase / Undecaprenyl-diphosphatase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsHuang, C.-Y. / Olieric, V. / Howe, N. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Vogeley, L. / Basu, S. / Diederichs, K. / Caffrey, M. / Wang, M.
Funding support Ireland, Switzerland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland16/IA/4435 Ireland
European Union701647 Switzerland
CitationJournal: Commun Biol / Year: 2018
Title: In situ serial crystallography for rapid de novo membrane protein structure determination.
Authors: Huang, C.Y. / Olieric, V. / Howe, N. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Vogeley, L. / Basu, S. / Diederichs, K. / Caffrey, M. / Wang, M.
History
DepositionFeb 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.2Mar 22, 2023Group: Database references / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Undecaprenyl-diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,05111
Polymers30,8881
Non-polymers3,16410
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint2 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.390, 144.370, 40.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-302-

TRS

-
Components

#1: Protein Undecaprenyl-diphosphatase / / Bacitracin resistance protein / Undecaprenyl pyrophosphate phosphatase


Mass: 30887.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: uppP, bacA, upk, b3057, JW3029 / Production host: Escherichia coli (E. coli)
References: UniProt: P60932, UniProt: P60933*PLUS, undecaprenyl-diphosphate phosphatase
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 40 % PEG-400, 0.3-0.5 M ammonium citrate dibasic and 0.1 M sodium citrate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2.3→40.39 Å / Num. obs: 15224 / % possible obs: 100 % / Redundancy: 16.95 % / Rrim(I) all: 0.5 / Net I/σ(I): 9.85
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 14.09 % / Num. unique obs: 2127 / CC1/2: 0.99 / Rrim(I) all: 6.39 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXDEphasing
CRANK2phasing
RefinementResolution: 2.3→40.39 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2224 761 5 %
Rwork0.194 --
obs0.1954 15224 99.94 %
Refinement stepCycle: LAST / Resolution: 2.3→40.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 197 65 2316

+
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