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- PDB-4p6h: Tl+-bound inward-facing state (bound conformation) of the glutama... -

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Basic information

Entry
Database: PDB / ID: 4p6h
TitleTl+-bound inward-facing state (bound conformation) of the glutamate transporter homologue GltPh
ComponentsGltPh
KeywordsTRANSPORT 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
Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1.
Similarity search - Domain/homology
: / THALLIUM (I) ION / Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.08 Å
AuthorsVerdon, G. / Boudker, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health - NINDSNS064357 United States
CitationJournal: Elife / Year: 2014
Title: Coupled ion binding and structural transitions along the transport cycle of glutamate transporters.
Authors: Verdon, G. / Oh, S. / Serio, R.N. / Boudker, O.
History
DepositionMar 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GltPh
B: GltPh
C: GltPh
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,67612
Polymers133,8483
Non-polymers1,8289
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-184 kcal/mol
Surface area48220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.830, 200.434, 206.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 700
2111B1 - 700
3111C1 - 700

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Components

#1: Protein GltPh


Mass: 44615.910 Da / Num. of mol.: 3 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1295 / Production host: Escherichia coli (E. coli) / Strain (production host): DH10 / References: UniProt: O59010
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-TL / THALLIUM (I) ION / Thallium


Mass: 204.383 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Tl

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.28 Å3/Da / Density % sol: 71.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG 400, Potassium Citrate, Potassium Chloride, Magnesium Chloride
PH range: 5.0 - 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 4→100 Å / Num. obs: 23932 / % possible obs: 65.3 % / Redundancy: 3.4 % / Net I/σ(I): 7.9
Reflection shellResolution: 4→4.14 Å / % possible obs: 6.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KBC

3kbc


Resolution: 4.08→15 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.874 / Cross valid method: THROUGHOUT / ESU R Free: 1.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2962 1222 9.9 %RANDOM
Rwork0.25841 ---
obs0.26214 11105 67.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 135.155 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0 Å2
2--1.38 Å20 Å2
3----1.31 Å2
Refinement stepCycle: 1 / Resolution: 4.08→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8985 0 9 0 8994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229159
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.98512513
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76551227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.99523.765255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.56151443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9631518
X-RAY DIFFRACTIONr_chiral_restr0.0750.21596
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216552
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.1971.56078
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.41229783
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.70433081
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3274.52730
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2998 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional00.01
Btight positional00.01
Ctight positional00.01
Atight thermal0.030.5
Btight thermal0.030.5
Ctight thermal0.020.5
LS refinement shellResolution: 4.077→4.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 8 -
Rwork0.289 72 -
obs--6.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.75063.5518-0.10557.69641.31114.71521.07140.57710.7533-0.6256-0.61840.01911.69711.9008-0.4531.23581.18130.00461.1776-0.07170.123764.349-20.5622.269
29.8563-0.6621-4.20182.69190.70589.09020.290.17220.5199-0.4282-0.13460.3963-0.5318-1.3795-0.15530.18680.20230.11310.37640.18410.370638.136-6.76731.407
33.1053-4.35610.293514.8631-1.16579.08920.25270.1514-0.5295-0.22760.4007-0.24552.8706-1.9239-0.65350.9589-0.6246-0.16160.5219-0.13720.713239.927-37.61630.595
44.55751.5942-0.03275.43083.27877.674-0.15880.1376-0.9365-0.55580.039-0.49991.06010.45470.11990.91450.80950.2021.119-0.11840.749573.735-32.09315.014
57.3176-0.8251-1.18924.9056-1.110812.74770.6071.0251.3182-0.111-0.60350.0332-2.9689-0.7472-0.00351.21430.40010.58510.27730.3030.984141.1578.82526.755
610.9289-0.3861-0.52054.7289-1.32112.6035-0.10241.1603-0.5636-0.43930.35421.20051.222-2.2606-0.25191.535-1.1021-0.42431.10550.01761.285523.968-41.77532.032
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 74
2X-RAY DIFFRACTION1A129 - 224
3X-RAY DIFFRACTION2B7 - 74
4X-RAY DIFFRACTION2B129 - 224
5X-RAY DIFFRACTION3C7 - 74
6X-RAY DIFFRACTION3C129 - 224
7X-RAY DIFFRACTION4A75 - 128
8X-RAY DIFFRACTION4A223 - 700
9X-RAY DIFFRACTION5B75 - 128
10X-RAY DIFFRACTION5B223 - 700
11X-RAY DIFFRACTION6C75 - 128
12X-RAY DIFFRACTION6C223 - 700

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