[English] 日本語
Yorodumi
- PDB-8dfk: X-ray crystal structure of Bacillus subtilis ComEA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dfk
TitleX-ray crystal structure of Bacillus subtilis ComEA
ComponentsComE operon protein 1
KeywordsDNA BINDING PROTEIN / plasma membrane / DNA binding / genetic competence / oligomerization
Function / homology
Function and homology information


establishment of competence for transformation / protein secretion by the type II secretion system / type II protein secretion system complex / DNA repair / DNA binding / plasma membrane
Similarity search - Function
Competence protein ComEA / Competence protein ComEA, helix-hairpin-helix domain / RuvA domain 2-like / Soluble ligand binding domain / SLBB domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1
Similarity search - Domain/homology
ComE operon protein 1
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsAhmed, I. / Khaja, F.T. / Neiditch, M.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM057720 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structure-function studies reveal ComEA contains an oligomerization domain essential for transformation in gram-positive bacteria.
Authors: Ahmed, I. / Hahn, J. / Henrickson, A. / Khaja, F.T. / Demeler, B. / Dubnau, D. / Neiditch, M.B.
History
DepositionJun 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ComE operon protein 1
B: ComE operon protein 1
C: ComE operon protein 1
D: ComE operon protein 1
E: ComE operon protein 1
F: ComE operon protein 1
G: ComE operon protein 1


Theoretical massNumber of molelcules
Total (without water)117,1637
Polymers117,1637
Non-polymers00
Water0
1
A: ComE operon protein 1
B: ComE operon protein 1


Theoretical massNumber of molelcules
Total (without water)33,4752
Polymers33,4752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ComE operon protein 1
D: ComE operon protein 1


Theoretical massNumber of molelcules
Total (without water)33,4752
Polymers33,4752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: ComE operon protein 1
F: ComE operon protein 1


Theoretical massNumber of molelcules
Total (without water)33,4752
Polymers33,4752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: ComE operon protein 1
G: ComE operon protein 1


Theoretical massNumber of molelcules
Total (without water)33,4752
Polymers33,4752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.525, 116.482, 183.268
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 60 through 122)
d_2ens_1(chain "B" and resid 60 through 122)
d_3ens_1(chain "C" and resid 60 through 122)
d_4ens_1(chain "D" and resid 60 through 122)
d_5ens_1(chain "E" and resid 60 through 122)
d_6ens_1(chain "F" and resid 60 through 122)
d_7ens_1chain "G"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUGLUA2 - 64
d_21ens_1GLUGLUB2 - 64
d_31ens_1GLUGLUC2 - 64
d_41ens_1GLUGLUD2 - 64
d_51ens_1GLUGLUE2 - 64
d_61ens_1GLUGLUF2 - 64
d_71ens_1GLUGLUG1 - 63

NCS oper:
IDCodeMatrixVector
1given(0.999933947875, 0.00970867786597, 0.00615154131853), (-0.00679596416465, 0.931069966014, -0.364777374927), (-0.00926902139233, 0.364711474952, 0.931074446691)0.700861473459, -1.23722270678, 18.8754901361
2given(0.999886388166, 0.014374798771, 0.00453606886316), (-0.00556411609068, 0.631658623273, -0.775226692173), (-0.0140089747151, 0.775113378033, 0.631666842427)0.922541378025, -21.4098016849, 43.7126921977
3given(0.999643822574, 0.0158875782308, 0.0214432471424), (0.0182768901514, 0.177939277581, -0.983871723743), (-0.0194469348856, 0.983913206717, 0.177585524105)1.30178402131, -50.0238286813, 55.7129550193
4given(0.99984790132, 0.0158106058091, 0.00736199497339), (0.0106376255945, -0.218338336997, -0.975815152331), (-0.0138208229766, 0.975745046281, -0.21847331533)0.632044998654, -71.3076916611, 56.6664758396
5given(0.996170753373, 0.0795947668651, 0.0361732388964), (0.0768321187615, -0.599545949055, -0.796643885622), (-0.041721165506, 0.796372606296, -0.603365574332)7.11145415548, -92.5227957126, 46.8138731362
6given(0.998731950729, 0.0341939355902, -0.0369494974422), (0.0118012327116, -0.872508370031, -0.488456625641), (-0.0489410001825, 0.487401188955, -0.87180551702)1.83762031014, -109.51464701, 30.4109088452

-
Components

#1: Protein
ComE operon protein 1


Mass: 16737.549 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: comEA, comE1, BSU25590 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39694

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 500, 0.1 M succinate [pH 5.5]

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 20483 / % possible obs: 99.5 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 13.15
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 1011 / CC1/2: 0.516

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→36.01 Å / SU ML: 0.4627 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3393
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.276 1991 9.74 %
Rwork0.2541 18450 -
obs0.2562 20441 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 0 0 3359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283387
X-RAY DIFFRACTIONf_angle_d0.54624574
X-RAY DIFFRACTIONf_chiral_restr0.0494531
X-RAY DIFFRACTIONf_plane_restr0.0027614
X-RAY DIFFRACTIONf_dihedral_angle_d5.252468
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.492554452788
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.606967528423
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.57253854064
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.552527696953
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.638935494104
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.809961573781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.41631350.37171262X-RAY DIFFRACTION96.08
3.28-3.370.33251460.31931299X-RAY DIFFRACTION99.66
3.37-3.470.33591380.29271305X-RAY DIFFRACTION99.65
3.47-3.580.31261360.29371319X-RAY DIFFRACTION99.59
3.58-3.710.28141460.28881315X-RAY DIFFRACTION100
3.71-3.850.28251420.28111292X-RAY DIFFRACTION99.58
3.85-4.030.2171420.26921308X-RAY DIFFRACTION98.77
4.03-4.240.27861400.26881295X-RAY DIFFRACTION98.02
4.24-4.510.25961410.25891322X-RAY DIFFRACTION99.93
4.51-4.850.25921440.24421328X-RAY DIFFRACTION99.93
4.85-5.340.26031470.22261331X-RAY DIFFRACTION99.66
5.34-6.110.24091410.23971344X-RAY DIFFRACTION99.73
6.11-7.690.28171460.23931342X-RAY DIFFRACTION99.2
7.69-36.010.27631470.22091388X-RAY DIFFRACTION97.65

+
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