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- PDB-8en9: TehA native-SAD structure determined at 5 keV with a helium envir... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


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


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

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Experimental details

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Experiment

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

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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

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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

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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

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