[English] 日本語
Yorodumi
- PDB-8en9: TehA native-SAD structure determined at 5 keV with a helium envir... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8en9
TitleTehA native-SAD structure determined at 5 keV with a helium environment
ComponentsTellurite resistance protein TehA homolog
KeywordsMEMBRANE PROTEIN / anomalous diffration / native SAD / low energy / helium path
Function / homology
Function and homology information


monoatomic cation efflux transmembrane transporter activity / response to tellurium ion / response to antibiotic / identical protein binding / plasma membrane
Similarity search - Function
Tellurite resistance protein TehA/malic acid transport protein / Tellurite resistance protein TehA / Transporter protein SLAC1/Mae1/ Ssu1/TehA / Voltage-dependent anion channel superfamily / Voltage-dependent anion channel
Similarity search - Domain/homology
Tellurite resistance protein TehA homolog
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsKarasawa, A. / Andi, B. / Ruchs, M.R. / Shi, W. / McSweeney, S. / Hendrickson, W.A. / Liu, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116799 United States
CitationJournal: Iucrj / Year: 2022
Title: Multi-crystal native-SAD phasing at 5 keV with a helium environment.
Authors: Karasawa, A. / Andi, B. / Fuchs, M.R. / Shi, W. / McSweeney, S. / Hendrickson, W.A. / Liu, Q.
History
DepositionSep 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tellurite resistance protein TehA homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8089
Polymers35,2531
Non-polymers1,5568
Water1,06359
1
A: Tellurite resistance protein TehA homolog
hetero molecules

A: Tellurite resistance protein TehA homolog
hetero molecules

A: Tellurite resistance protein TehA homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,42527
Polymers105,7583
Non-polymers4,66724
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16100 Å2
ΔGint-59 kcal/mol
Surface area35370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.399, 95.399, 136.128
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-408-

NA

21A-554-

HOH

31A-556-

HOH

-
Components

#1: Protein Tellurite resistance protein TehA homolog


Mass: 35252.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: tehA, HI_0511 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P44741
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1 M HEPES, 1 mM zinc sulfate, 27-29% PEG400, 10 mM spermidine, 50 mM octyl glucoside

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 2.479 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.479 Å / Relative weight: 1
ReflectionResolution: 2.6→39.53 Å / Num. obs: 28275 / % possible obs: 99.8 % / Redundancy: 109.6 % / Biso Wilson estimate: 35.19 Å2 / CC1/2: 0.995 / Net I/σ(I): 24.4
Reflection shellResolution: 2.6→2.72 Å / Num. unique obs: 3438 / CC1/2: 0.482

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSv1-1545data reduction
Aimless0.5.17data scaling
PHASER2.5.7phasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.6→39.53 Å / SU ML: 0.3246 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.1378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2174 2841 10.09 %
Rwork0.1698 25322 -
obs0.1747 28163 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 103 59 2580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812597
X-RAY DIFFRACTIONf_angle_d0.90093532
X-RAY DIFFRACTIONf_chiral_restr0.0464411
X-RAY DIFFRACTIONf_plane_restr0.0067413
X-RAY DIFFRACTIONf_dihedral_angle_d19.6529876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.650.45461360.41331158X-RAY DIFFRACTION89.49
2.65-2.690.38591420.30621172X-RAY DIFFRACTION97.48
2.69-2.750.28351430.22981295X-RAY DIFFRACTION99.58
2.75-2.80.26181460.18891259X-RAY DIFFRACTION99.93
2.8-2.860.26121480.18561318X-RAY DIFFRACTION100
2.86-2.930.24461340.18211224X-RAY DIFFRACTION100
2.93-30.22031500.18081306X-RAY DIFFRACTION100
3-3.080.23051420.17021280X-RAY DIFFRACTION100
3.08-3.170.25671360.18351276X-RAY DIFFRACTION100
3.18-3.280.17981400.16221252X-RAY DIFFRACTION100
3.28-3.390.21851440.15251328X-RAY DIFFRACTION100
3.39-3.530.20381400.13981262X-RAY DIFFRACTION100
3.53-3.690.19181440.16041248X-RAY DIFFRACTION100
3.69-3.890.22511360.14381276X-RAY DIFFRACTION100
3.89-4.130.21091480.14231302X-RAY DIFFRACTION100
4.13-4.450.16031400.13071270X-RAY DIFFRACTION100
4.45-4.890.16681420.14761264X-RAY DIFFRACTION100
4.9-5.60.20961400.16591292X-RAY DIFFRACTION100
5.6-7.050.22711460.19571268X-RAY DIFFRACTION100
7.05-39.530.20191440.17661272X-RAY DIFFRACTION99.44

+
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