[English] 日本語
Yorodumi
- PDB-6hee: Crystal structure of Extracellular Domain 1 (ECD1) of FtsX from S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hee
TitleCrystal structure of Extracellular Domain 1 (ECD1) of FtsX from S. pneumonie in complex with undecyl-maltoside
ComponentsCell division protein FtsX
KeywordsCELL CYCLE / cell division / MEMBRANE PROTEIN
Function / homologyCell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / ABC3 transporter permease protein domain / FtsX-like permease family / cell division / plasma membrane / Cell division protein FtsX
Function and homology information
Biological speciesStreptococcus pneumoniae serotype 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsMartinez-Caballero, S. / Alcorlo-Pages, M. / Hermoso, J.A.
CitationJournal: Mbio / Year: 2019
Title: Structure of the Large Extracellular Loop of FtsX and Its Interaction with the Essential Peptidoglycan Hydrolase PcsB in Streptococcus pneumoniae.
Authors: Rued, B.E. / Alcorlo, M. / Edmonds, K.A. / Martinez-Caballero, S. / Straume, D. / Fu, Y. / Bruce, K.E. / Wu, H. / Havarstein, L.S. / Hermoso, J.A. / Winkler, M.E. / Giedroc, D.P.
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Cell division protein FtsX
B: Cell division protein FtsX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3665
Polymers26,6512
Non-polymers7153
Water37821
1
A: Cell division protein FtsX
hetero molecules

B: Cell division protein FtsX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3665
Polymers26,6512
Non-polymers7153
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2260 Å2
ΔGint-23 kcal/mol
Surface area14910 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-14 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.610, 84.610, 106.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Cell division protein FtsX


Mass: 13325.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Strain: D39 / NCTC 7466 / Gene: ftsX, SPD_0660 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04LE4
#2: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.57 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: ammonium sulfate, sodium and potassium tartrate and sodium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→42.31 Å / Num. obs: 17731 / % possible obs: 98.89 % / Redundancy: 22.1 % / Rpim(I) all: 0.004 / Net I/σ(I): 44.14
Reflection shellResolution: 2.3→2.38 Å / Rpim(I) all: 0.092

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementStarting model: 6HE6

6he6


Resolution: 2.3→42.31 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.18
RfactorNum. reflection% reflection
Rfree0.2976 922 5.2 %
Rwork0.2607 --
obs0.2626 17717 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 47 21 1800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081799
X-RAY DIFFRACTIONf_angle_d0.9872429
X-RAY DIFFRACTIONf_dihedral_angle_d5.1641086
X-RAY DIFFRACTIONf_chiral_restr0.062278
X-RAY DIFFRACTIONf_plane_restr0.006310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.42130.40911360.32132332X-RAY DIFFRACTION100
2.4213-2.5730.30521370.30612333X-RAY DIFFRACTION100
2.573-2.77170.38761360.29822348X-RAY DIFFRACTION100
2.7717-3.05050.36081330.30342370X-RAY DIFFRACTION100
3.0505-3.49180.33651170.28642408X-RAY DIFFRACTION100
3.4918-4.39870.28781230.2342432X-RAY DIFFRACTION100
4.3987-44.98160.2531400.24542572X-RAY DIFFRACTION100

+
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