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- PDB-1xfh: Structure of glutamate transporter homolog from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 1xfh
TitleStructure of glutamate transporter homolog from Pyrococcus horikoshii
Componentsproton glutamate symport protein
KeywordsTRANSPORT PROTEIN / Trimeric helical transmembrane protein
Function / homology
Function and homology information


amino acid:sodium symporter activity / L-aspartate transmembrane transport / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / chloride transmembrane transporter activity / protein homotrimerization / chloride transmembrane transport / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Proton glutamate symport protein / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.5 Å
AuthorsYernool, D. / Boudker, O. / Jin, Y. / Gouaux, E.
CitationJournal: Nature / Year: 2004
Title: Structure of a glutamate transporter homologue from Pyrococcus horikoshii
Authors: Yernool, D. / Boudker, O. / Jin, Y. / Gouaux, E.
History
DepositionSep 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: proton glutamate symport protein
B: proton glutamate symport protein
C: proton glutamate symport protein


Theoretical massNumber of molelcules
Total (without water)133,9263
Polymers133,9263
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-66 kcal/mol
Surface area46140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.000, 116.000, 322.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALASNASNAA12 - 10812 - 108
21VALVALASNASNBB12 - 10812 - 108
31VALVALASNASNCC12 - 10812 - 108
42PROPROGLUGLUAA129 - 416129 - 416
52PROPROGLUGLUBB129 - 416129 - 416
62PROPROGLUGLUCC129 - 416129 - 416
DetailsThe asymmetric unit contains the biological relevant trimer

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Components

#1: Protein proton glutamate symport protein / glutamate transporter homolog


Mass: 44641.945 Da / Num. of mol.: 3 / Mutation: D37H, K40H, K125H, K132H, K223H, K264H, E368H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: GltPh / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: O59010

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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: 3.5 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4
Details: PEG 1000, Na/K phosphate, citrate, decyl maltoside, pH 4.0, VAPOR DIFFUSION
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-10 mg/mlprotein1drop
214-18 %PEG10001reservoir
3100 mM1reservoirLi2SO4
450 mMcitric acid1reservoir
550 mMsodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.10, 1.0711, 0.9918, 1.0721
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2003 / Details: mono/mirrors
RadiationMonochromator: Silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.07111
30.99181
41.07211
ReflectionResolution: 3.5→10 Å / Num. all: 30892 / Num. obs: 30587 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 7.3
Reflection shellResolution: 3.5→3.65 Å / Redundancy: 4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 0.7 / Rsym value: 0.84
Reflection
*PLUS
% possible obs: 99 % / Redundancy: 6.7 %
Reflection shell
*PLUS
% possible obs: 98 % / Redundancy: 4.4 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.5→10 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.907 / SU B: 38.389 / SU ML: 0.579 / Cross valid method: THROUGHOUT / ESU R Free: 0.627 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Ramachandran plot: Favored (%) = 79.2; Allowed (%) = 20.0; Generously allowed (%) = 0.8 and Disallowed (%) = 0.0.
RfactorNum. reflection% reflectionSelection details
Rfree0.3091 1428 5 %RANDOM
Rwork0.28988 ---
obs0.29086 27199 97.1 %-
all-27199 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 124.432 Å2
Baniso -1Baniso -2Baniso -3
1-4.83 Å22.41 Å20 Å2
2--4.83 Å20 Å2
3----7.24 Å2
Refinement stepCycle: LAST / Resolution: 3.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8652 0 0 0 8652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228811
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.97412054
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.94851212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.21536
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026402
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2610.35355
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.5605
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.34
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.03626003
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.86539537
X-RAY DIFFRACTIONr_scbond_it0.75922808
X-RAY DIFFRACTIONr_scangle_it1.23132517
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1540tight positional0.170.2
2B1540tight positional0.160.2
3C1540tight positional0.150.2
1A1214medium positional0.272
2B1214medium positional0.272
3C1214medium positional0.262
1A1540tight thermal16.523
2B1540tight thermal9.843
3C1540tight thermal8.213
1A1214medium thermal16.8810
2B1214medium thermal10.1210
3C1214medium thermal8.4310
LS refinement shellResolution: 3.5→3.58 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.409 89
Rwork0.37 1739
Software
*PLUS
Version: 5.1.24 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.409 / Rfactor Rwork: 0.37

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