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- PDB-3m72: Crystal Structure of Plant SLAC1 homolog TehA -

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Basic information

Entry
Database: PDB / ID: 3m72
TitleCrystal Structure of Plant SLAC1 homolog TehA
ComponentsTellurite resistance protein tehA homolog
KeywordsStructural Genomics / Unknown function / anion channel / alpha helical integral membrane protein / PSI-2 / Protein Structure Initiative / New York Consortium on Membrane Protein Structure / NYCOMPS / Plant SLAC-1 Homolog
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
Voltage-dependent anion channel / 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 / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Tellurite resistance protein TehA homolog
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsChen, Y.-H. / Hendrickson, W.A. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: To be Published
Title: Crystal Structure of Plant SLAC1 homolog TehA
Authors: Chen, Y.-H. / Hendrickson, W.A.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 6, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)36,7806
Polymers35,3191
Non-polymers1,4625
Water3,423190
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)110,34118
Polymers105,9563
Non-polymers4,38615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area16840 Å2
ΔGint-5 kcal/mol
Surface area33470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.731, 95.731, 136.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-367-

HOH

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Components

#1: Protein Tellurite resistance protein tehA homolog


Mass: 35318.648 Da / Num. of mol.: 1 / Mutation: A208P, G263P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: KW20 / Gene: HI0511, Rd, tehA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 298 K / pH: 7.8
Details: 28% PEG600, 50mM Hepe-Na pH7.8, 1mM ZnSO4, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 51595 / % possible obs: 99 % / Redundancy: 3.9 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 6.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.982 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.922 / SU ML: 0.042 / SU R Cruickshank DPI: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.174 2578 5.1 %RANDOM
Rwork0.143 ---
obs0.144 50615 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.641 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 100 190 2728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222739
X-RAY DIFFRACTIONr_bond_other_d00.022594
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9893748
X-RAY DIFFRACTIONr_angle_other_deg1.96336015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9565336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83722.5104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12915408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5011510
X-RAY DIFFRACTIONr_chiral_restr0.2160.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212946
X-RAY DIFFRACTIONr_gen_planes_other00.02607
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9911.51597
X-RAY DIFFRACTIONr_mcbond_other0.3891.5646
X-RAY DIFFRACTIONr_mcangle_it1.60122593
X-RAY DIFFRACTIONr_scbond_it2.42431142
X-RAY DIFFRACTIONr_scangle_it3.7614.51147
X-RAY DIFFRACTIONr_rigid_bond_restr1.19435333
X-RAY DIFFRACTIONr_sphericity_free6.2383196
X-RAY DIFFRACTIONr_sphericity_bonded1.90435239
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 202 -
Rwork0.235 3562 -
obs--99.84 %
Refinement TLS params.Method: refined / Origin x: 26.7578 Å / Origin y: -27.925 Å / Origin z: -6.5754 Å
111213212223313233
T0.0043 Å20.0001 Å2-0.0017 Å2-0.0565 Å2-0.0133 Å2--0.0331 Å2
L0.4248 °20.087 °2-0.0645 °2-0.3698 °20.1871 °2--0.5801 °2
S-0.0138 Å °0.0103 Å °0.0165 Å °-0.0059 Å °-0.0465 Å °0.1099 Å °0.0117 Å °-0.1403 Å °0.0603 Å °

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