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- PDB-4oyf: Crystal structure of GLTPH R397A IN Sodium-bound state -

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Basic information

Entry
Database: PDB / ID: 4oyf
TitleCrystal structure of GLTPH R397A IN Sodium-bound state
ComponentsGLUTAMATE SYMPORT PROTEIN
KeywordsTRANSPORT PROTEIN / ALPHA HELICAL / MEMBRANE PROTEIN / HELICAL HAIRPIN / UNWOUND REGION
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 / 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
Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.41 Å
AuthorsBoudker, O. / Oh, S. / Verdon, G. / Serio, R.
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 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMATE SYMPORT PROTEIN
B: GLUTAMATE SYMPORT PROTEIN
C: GLUTAMATE SYMPORT PROTEIN
D: GLUTAMATE SYMPORT PROTEIN
E: GLUTAMATE SYMPORT PROTEIN
F: GLUTAMATE SYMPORT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,99012
Polymers267,8526
Non-polymers1386
Water1086
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19050 Å2
ΔGint-249 kcal/mol
Surface area85130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.579, 110.579, 306.923
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.496943, -0.837607, -0.226854), (0.838038, -0.395363, -0.376005), (0.225255, -0.376966, 0.898419)329.86926, 284.28778, 76.98489
3given(-0.500302, 0.836925, 0.221932), (-0.836777, -0.401487, -0.372307), (-0.222491, -0.371974, 0.901184)-91.11951, 418.94342, 111.30257
4given(-0.501299, -0.836388, -0.221707), (-0.836218, 0.402449, 0.372524), (-0.222349, 0.372142, -0.90115)330.09027, 223.96692, -103.85536
5given(1, -1.6E-5, -6.3E-5), (-1.6E-5, -0.999999, -0.001028), (-6.3E-5, 0.001028, -0.999999)-0.00578, 510.65985, -28.14601
6given(-0.497213, 0.837441, 0.226875), (0.83778, 0.395404, 0.376539), (0.225622, 0.377291, -0.898191)-91.54331, 92.88789, -140.69576

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Components

#1: Protein
GLUTAMATE SYMPORT PROTEIN / GLTPH


Mass: 44641.945 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: PBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): DH10b / References: UniProt: O59010*PLUS
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG400 sodium chloride citrate/tris / PH range: 4.5

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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: Jun 13, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.41→12 Å / Num. obs: 48366 / % possible obs: 87.3 % / Redundancy: 11.8 % / Net I/σ(I): 13.8

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementResolution: 3.41→12 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.864 / SU B: 80.329 / SU ML: 0.529 / Cross valid method: THROUGHOUT / ESU R Free: 0.639 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29348 2573 5.1 %RANDOM
Rwork0.28427 ---
obs0.28474 48366 88.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 151.382 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å22.34 Å20 Å2
2--2.34 Å20 Å2
3----7.59 Å2
Refinement stepCycle: 1 / Resolution: 3.41→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17580 0 6 6 17592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01917898
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.98424402
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48552382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.82223.793522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.737152880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5261542
X-RAY DIFFRACTIONr_chiral_restr0.0930.23096
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112780
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
LS refinement shellResolution: 3.41→3.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 22 -
Rwork0.344 452 -
obs--12.18 %
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)
10.4041-0.35350.26180.3602-0.37161.0587-0.1724-0.07250.06270.0840.1283-0.18060.1782-0.63530.0440.1752-0.14130.05570.63470.14120.572254.1285244.594811.4782
20.31310.5673-0.4121.4248-0.98651.57740.05610.0039-0.16780.2324-0.00910.0499-0.3114-0.0433-0.0470.22440.12480.06820.2727-0.06960.420689.0099271.330318.6101
30.2304-0.2273-0.61320.49010.68322.1925-0.1471-0.15120.03610.08510.13620.28390.52180.15110.01090.42610.1151-0.07430.2325-0.04210.39295.4187228.67387.1758
40.17480.1610.3920.32020.5382.5642-0.16250.1807-0.0373-0.16370.13420.2199-0.57150.2070.02840.3564-0.07350.04290.2205-0.0320.403495.4313282.0288-35.0562
50.10630.2208-0.05590.5541-0.27560.5783-0.10660.0193-0.0629-0.10660.0804-0.1449-0.2087-0.54930.02620.21870.1984-0.08510.77350.16080.472154.1356266.0777-39.3525
60.2634-0.43120.38331.11-1.07061.69780.0697-0.00410.1973-0.2463-0.0110.01870.3878-0.1008-0.05870.2485-0.1014-0.06420.2562-0.07050.44489.0038239.386-46.4928
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 416
2X-RAY DIFFRACTION2B9 - 416
3X-RAY DIFFRACTION3C9 - 416
4X-RAY DIFFRACTION4D9 - 416
5X-RAY DIFFRACTION5E9 - 416
6X-RAY DIFFRACTION6F9 - 416

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