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- PDB-4oye: Crystal structure of GltPh R397A in apo -

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Basic information

Entry
Database: PDB / ID: 4oye
TitleCrystal structure of GltPh R397A in apo
Components425aa long hypothetical proton glutamate symport protein
KeywordsTRANSPORT PROTEIN / Transporter / alpha-helix / membrane protein
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
Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4 Å
AuthorsBoudker, O. / Oh, S.
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 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
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_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords / symmetry
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_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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 / _struct_keywords.text / _symmetry.Int_Tables_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 425aa long hypothetical proton glutamate symport protein
B: 425aa long hypothetical proton glutamate symport protein
C: 425aa long hypothetical proton glutamate symport protein
D: 425aa long hypothetical proton glutamate symport protein
E: 425aa long hypothetical proton glutamate symport protein
F: 425aa long hypothetical proton glutamate symport protein
G: 425aa long hypothetical proton glutamate symport protein
H: 425aa long hypothetical proton glutamate symport protein
I: 425aa long hypothetical proton glutamate symport protein
J: 425aa long hypothetical proton glutamate symport protein
K: 425aa long hypothetical proton glutamate symport protein
L: 425aa long hypothetical proton glutamate symport protein


Theoretical massNumber of molelcules
Total (without water)516,09612
Polymers516,09612
Non-polymers00
Water00
1
A: 425aa long hypothetical proton glutamate symport protein
B: 425aa long hypothetical proton glutamate symport protein
C: 425aa long hypothetical proton glutamate symport protein
D: 425aa long hypothetical proton glutamate symport protein
E: 425aa long hypothetical proton glutamate symport protein
F: 425aa long hypothetical proton glutamate symport protein


Theoretical massNumber of molelcules
Total (without water)258,0486
Polymers258,0486
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18960 Å2
ΔGint-177 kcal/mol
Surface area87590 Å2
MethodPISA
2
G: 425aa long hypothetical proton glutamate symport protein
H: 425aa long hypothetical proton glutamate symport protein
I: 425aa long hypothetical proton glutamate symport protein
J: 425aa long hypothetical proton glutamate symport protein
K: 425aa long hypothetical proton glutamate symport protein
L: 425aa long hypothetical proton glutamate symport protein


Theoretical massNumber of molelcules
Total (without water)258,0486
Polymers258,0486
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19100 Å2
ΔGint-177 kcal/mol
Surface area87680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.365, 424.422, 113.985
Angle α, β, γ (deg.)90.00, 119.38, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.411451, 0.266706, -0.871537), (0.43731, 0.896739, 0.067965), (0.799667, -0.353168, -0.485597)227.0757, -21.51569, 350.22598
3given(-0.410566, 0.431787, 0.803116), (0.256576, 0.899892, -0.352652), (-0.874988, 0.061274, -0.480251)-178.28055, 82.31268, 367.94144
4given(-0.501088, -0.037606, 0.864579), (-0.032416, -0.997539, -0.062176), (0.864789, -0.059182, 0.498636)-186.0349, 38.93291, 108.94023
5given(-0.557551, -0.198139, -0.80615), (-0.191752, -0.914098, 0.35729), (-0.807693, 0.353788, 0.471663)218.84311, -60.83761, 134.49908
6given(0.88618, -0.463025, 0.017108), (-0.463058, -0.886325, -0.002227), (0.016195, -0.005948, -0.999851)2.87447, 29.40884, 481.27985
7given(0.415016, -0.43696, 0.798015), (-0.256084, -0.89776, -0.358397), (0.873031, -0.055618, -0.484483)-187.71445, -3.49213, 347.19122
8given(-0.999956, -0.001047, 0.009299), (0.000962, -0.999958, -0.009137), (0.009309, -0.009128, 0.999915)-0.96832, -82.24641, 32.53768
9given(0.408853, -0.257349, -0.875563), (-0.433847, -0.898878, 0.061613), (-0.80288, 0.35467, -0.479159)176.74509, -93.11244, 363.60455
10given(0.50672, 0.03232, 0.861504), (0.031753, 0.997919, -0.056114), (-0.861525, 0.05579, 0.50464)-154.44954, 119.55927, 130.08594
11given(0.551367, 0.204768, -0.808742), (0.192458, 0.912042, 0.362133), (0.81176, -0.355317, 0.463461)209.06114, 26.58334, 121.05167
12given(-0.886881, 0.461448, 0.022551), (0.461569, 0.887105, 0.000178), (-0.019923, 0.010566, -0.999746)42.13939, 102.96155, 448.78857

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Components

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


Mass: 43007.984 Da / Num. of mol.: 12 / Fragment: UNP residues 8-416
Mutation: D37H, K40H, K125H, K132H, K223H, K264H, E368H, R397A
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 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): DH10b / References: UniProt: O59010

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.59 Å3/Da / Density % sol: 73.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG400 Choline chloride citrate/tris

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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: Jul 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 4→20 Å / Num. obs: 52068 / % possible obs: 70.26 % / Redundancy: 2 % / Net I/σ(I): 12.3

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementResolution: 4→20 Å / Cor.coef. Fo:Fc: 0.863 / Cor.coef. Fo:Fc free: 0.85 / SU B: 110.309 / SU ML: 0.638 / Cross valid method: THROUGHOUT / ESU R Free: 1.004 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26648 2754 5 %RANDOM
Rwork0.24904 ---
obs0.24993 52068 70.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 137.224 Å2
Baniso -1Baniso -2Baniso -3
1--5.52 Å20 Å2-2.6 Å2
2--15.49 Å20 Å2
3----5.21 Å2
Refinement stepCycle: 1 / Resolution: 4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35277 0 0 0 35277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01935937
X-RAY DIFFRACTIONr_bond_other_d0.0020.0236546
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.98349126
X-RAY DIFFRACTIONr_angle_other_deg0.917383432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48754821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25123.7791003
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.976155578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2351572
X-RAY DIFFRACTIONr_chiral_restr0.0660.26309
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02140031
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027477
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: 4→4.101 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 15 -
Rwork0.288 503 -
obs--9.33 %
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)
10.91780.97630.25861.61810.48251.29080.0269-0.0604-0.19280.5274-0.0465-0.07490.00480.09750.01970.9714-0.1742-0.14210.2290.17640.579317.4526-14.415267.565
21.00260.5564-0.70191.4961-0.75621.3168-0.0084-0.0403-0.0618-0.2743-0.0412-0.36010.1999-0.02640.04960.86990.04250.02820.01540.06140.888223.3385-20.238223.3172
30.1462-0.1260.13971.9224-0.01520.34920.0380.0882-0.0750.0760.05290.31820.0154-0.193-0.09090.7436-0.12880.06520.5048-0.04770.9649-17.353-8.5005239.4168
40.9047-0.4004-0.08031.1232-0.77791.31460.0585-0.15920.08070.32310.0092-0.2681-0.16870.1371-0.06770.9249-0.3751-0.32240.29290.06480.632536.978235.975258.3551
51.74410.9679-0.62991.3638-0.15150.60050.09590.1320.23680.2972-0.01690.334-0.3764-0.1433-0.07910.95990.08850.09970.0377-0.010.7668-4.172144.379241.7967
60.3111-0.2573-0.65212.13760.59871.51920.0201-0.1104-0.0281-0.3138-0.0374-0.4187-0.17310.15690.01720.8869-0.04070.07270.140.23010.828129.654433.1871213.9811
71.13970.1852-0.70772.05690.23010.7645-0.1329-0.3554-0.03170.02750.3667-0.3849-0.15070.5997-0.23380.7198-0.18370.07750.5743-0.17730.981418.4208-75.5891206.1233
80.88120.8551-0.27871.7014-0.46011.53940.02260.07120.25670.3872-0.07340.15840.0853-0.17880.05080.8989-0.14620.09550.2014-0.29550.773-16.1681-70.1856234.611
91.1240.5550.34331.73091.08860.7311-0.07110.02440.0999-0.4596-0.0550.2425-0.3592-0.02930.12611.0370.1301-0.13180.0234-0.06040.8241-22.2289-63.8874190.324
100.696-0.4107-0.0651.56181.05051.18230.2194-0.0580.01190.4249-0.21050.38040.4155-0.1875-0.00890.9427-0.45120.33460.2454-0.18370.7513-35.6326-120.2682225.0023
111.58830.99820.09132.00910.22590.70860.03290.125-0.13530.36360.2301-0.310.43880.2022-0.2630.85480.1569-0.11690.0957-0.11990.66555.4684-128.4675208.1039
120.1474-0.13580.17132.5793-0.48851.9480.07890.0322-0.0112-0.2492-0.1020.42290.0599-0.20840.02320.83590.0235-0.11480.1402-0.25230.7288-28.5921-117.2284180.5614
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 416
2X-RAY DIFFRACTION2B8 - 416
3X-RAY DIFFRACTION3C8 - 416
4X-RAY DIFFRACTION4D8 - 416
5X-RAY DIFFRACTION5E8 - 416
6X-RAY DIFFRACTION6F8 - 416
7X-RAY DIFFRACTION7G8 - 416
8X-RAY DIFFRACTION8H8 - 416
9X-RAY DIFFRACTION9I8 - 416
10X-RAY DIFFRACTION10J8 - 416
11X-RAY DIFFRACTION11K8 - 416
12X-RAY DIFFRACTION12L8 - 416

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