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- PDB-4p1a: Thallium-bound inward-facing state of the glutamate transporter h... -

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Basic information

Entry
Database: PDB / ID: 4p1a
TitleThallium-bound inward-facing state of the glutamate transporter homologue GltPh
ComponentsGltPh
KeywordsTRANSPORT PROTEIN / membrane protein / sodium-couple / asparate transporter / inward-facing state / Thallium binding sites
Function / homology
Function and homology information


L-aspartate transmembrane transport / amino acid:sodium symporter activity / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / chloride transmembrane transporter activity / protein homotrimerization / chloride transmembrane transport / metal ion binding / identical protein 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
: / THALLIUM (I) ION / Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.75 Å
AuthorsVerdon, G. / Boudker, O.
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
DepositionFeb 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 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
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-180 kcal/mol
Surface area46830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.979, 196.564, 206.499
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
1111A10 - 601
2111B10 - 601
3111C10 - 601

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.345317, -0.821164, 0.454363), (0.823349, -0.497427, -0.273246), (0.450392, 0.279743, 0.847874)-66.14637, -1.90089, 22.13398
3given(-0.357296, 0.819762, 0.447583), (-0.817194, -0.506425, 0.275185), (0.452253, -0.26744, 0.850848)-31.7457, -61.58086, 10.64987

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Components

#1: Protein GltPh / 425aa long hypothetical proton glutamate symport protein


Mass: 44615.910 Da / Num. of mol.: 3 / Fragment: Residues 1-417 / 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 K-12 (bacteria) / Strain (production host): DH10 / References: UniProt: O59010
#2: Chemical
ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Tl
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.06 Å3/Da / Density % sol: 69.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion
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 315 / 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: 3.75→100 Å / Num. obs: 44497 / % possible obs: 99.7 % / Redundancy: 3.8 % / Net I/σ(I): 8.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P19

4p19


Resolution: 3.75→15 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.925 / SU B: 82.052 / SU ML: 0.528 / Cross valid method: THROUGHOUT / ESU R Free: 0.64 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 1161 5.1 %RANDOM
Rwork0.23046 ---
obs0.23189 21543 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 141.839 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9114 0 9 0 9123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199291
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.98212679
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40951231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50123.741278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.582151494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0141524
X-RAY DIFFRACTIONr_chiral_restr0.1190.21600
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216672
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 3013 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A5.33
B4.91
C6.31
LS refinement shellResolution: 3.75→3.841 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 82 -
Rwork0.299 1462 -
obs--99.68 %
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)
13.71591.3267-0.32957.96020.10180.690.374-0.9721-0.4070.083-0.4584-0.08180.35860.32580.08440.8465-0.032-0.04941.51510.17120.3121-37.9168-36.634-30.1924
25.1593-2.4713-1.30053.3483-0.12421.22810.4214-0.86450.15380.2547-0.24410.1591-0.07070.0393-0.17731.0131-0.27740.05951.4949-0.06960.3416-61.8047-20.8141-22.2293
37.20591.4333-3.49082.28910.12642.4590.3528-0.99940.65890.0201-0.2089-0.2177-0.46190.607-0.14391.0338-0.32220.15841.499-0.32690.5231-36.5209-6.7882-30.6471
46.88351.00822.22971.3097-0.42581.30560.0221-1.0345-0.3658-0.0757-0.2723-0.189-0.1201-0.20110.25031.14560.1073-0.04791.6910.27980.7972-23.5381-40.88-35.8338
51.8665-1.56540.67174.6554-3.93094.9090.1555-0.5723-0.2443-0.0948-0.0882-0.1041-0.38230.24-0.06730.9989-0.2781-0.0061.64120.12080.6174-73.0257-31.6943-19.5381
63.7613-0.8703-4.04150.39110.64525.44020.8496-0.97571.68250.07410.3296-0.3827-0.77520.6366-1.17921.6989-0.28330.49341.6153-0.68391.5978-40.92718.6162-30.3295
76.00433.51092.24816.3172-1.24456.04290.012-0.9586-0.62650.119-0.3763-0.1705-0.08940.49910.36431.03990.1093-0.12452.23020.52720.7026-18.493-44.591-16.1868
87.2004-2.22852.31117.176-2.73927.3861-0.2155-1.5389-0.26630.72530.07450.3126-0.9771-0.16350.1411.2547-0.37280.17462.18170.12320.5043-68.8919-28.60960.8553
910.04173.83721.16913.90582.56979.52010.3393-1.77891.8603-0.0964-0.0441-0.3978-1.30161.4829-0.29531.7016-0.430.18442.9908-1.2831.5154-30.75419.4542-12.2148
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 76
2X-RAY DIFFRACTION1A130 - 221
3X-RAY DIFFRACTION2B1 - 76
4X-RAY DIFFRACTION2B130 - 221
5X-RAY DIFFRACTION3C1 - 76
6X-RAY DIFFRACTION3C130 - 221
7X-RAY DIFFRACTION4A77 - 129
8X-RAY DIFFRACTION4A222 - 256
9X-RAY DIFFRACTION4A314 - 601
10X-RAY DIFFRACTION5B77 - 129
11X-RAY DIFFRACTION5B222 - 256
12X-RAY DIFFRACTION5B314 - 601
13X-RAY DIFFRACTION6C77 - 129
14X-RAY DIFFRACTION6C222 - 256
15X-RAY DIFFRACTION6C314 - 601
16X-RAY DIFFRACTION7A257 - 313
17X-RAY DIFFRACTION8B257 - 313
18X-RAY DIFFRACTION9C257 - 313

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