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- PDB-4p3j: Apo inward-facing state of the glutamate transporter homologue Gl... -

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Basic information

Entry
Database: PDB / ID: 4p3j
TitleApo inward-facing state of the glutamate transporter homologue GltPh in alkali-free conditions
ComponentsGltPh
KeywordsTRANSPORT PROTEIN / membrane protein / sodium-couple asparate transporter / inward-facing state / apo form / alkali-free conditions
Function / homology
Function and homology information


L-aspartate transmembrane transport / L-aspartate transmembrane transporter activity / amino acid:sodium symporter 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 / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsVerdon, G. / Boudker, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health (NINDS)NS064357 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 8, 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)134,4506
Polymers133,8483
Non-polymers6023
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-147 kcal/mol
Surface area47300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.948, 196.843, 207.484
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
12A
22B
32C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A6 - 255
2111B6 - 255
3111C6 - 255
1211A315 - 416
2211B315 - 416
3211C315 - 416
1121A255 - 314
2121B255 - 314
3121C255 - 314

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.330127, -0.815525, -0.475327), (0.820192, -0.497076, 0.283197), (-0.467228, -0.296368, 0.832985)64.1804, 2.8138, 22.68006
3given(-0.353956, 0.813119, -0.462118), (-0.808494, -0.514409, -0.285867), (-0.470162, 0.272435, 0.83948)30.53713, 60.85577, 10.82581

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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: D37H, K40H, K55C, K125H, K132H, K223H, K264H, C321A, A364C, E368H
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-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: 4.08 Å3/Da / Density % sol: 69.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: PEG 400 Potassium Citrate Potassium Chloride Magnesium Chloride

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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: Mar 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.5→100 Å / Num. obs: 50777 / % possible obs: 94.4 % / Redundancy: 3.3 % / Net I/σ(I): 13.7
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 1.24

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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: 3.5→15 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.913 / SU B: 82.173 / SU ML: 0.549 / Cross valid method: THROUGHOUT / ESU R Free: 0.602 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27845 1353 5 %RANDOM
Rwork0.26317 ---
obs0.26395 25446 95.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 144.258 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20 Å2
2--6.38 Å20 Å2
3----8.2 Å2
Refinement stepCycle: 1 / Resolution: 3.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9088 0 3 0 9091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0199265
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.98112643
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.85351227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91723.741278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.604151490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.551524
X-RAY DIFFRACTIONr_chiral_restr0.0770.21594
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216656
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

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A25726.65
11B25728.48
11C25729.9
22A44215.73
22B44215.07
22C44226.35
LS refinement shellResolution: 3.5→3.586 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 73 -
Rwork0.355 1723 -
obs--93.2 %
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)
11.14110.63160.40932.0484-0.4830.58370.2746-0.5950.12510.0592-0.3075-0.0641-0.0727-0.28190.0330.3774-0.06240.17770.3686-0.12610.329637.461136.6613-30.4686
21.60710.13890.00350.15550.18280.93150.3745-0.3948-0.04110.159-0.2745-0.00050.08940.0181-0.10.2857-0.2821-0.02590.49340.01220.195861.316620.9937-22.1455
30.989-0.04730.4920.2147-0.06230.51410.2222-0.3411-0.26270.0696-0.17010.08120.3244-0.1852-0.05210.3795-0.277-0.10080.37070.13260.351736.40326.8535-30.9345
41.28440.2079-2.12850.8512-0.16244.44320.0787-0.30620.3187-0.1373-0.18920.195-0.0960.13140.11060.15550.1240.11210.3928-0.24620.570522.079741.9104-32.0963
50.595-0.609-0.43971.16110.96913.0130.1604-0.24570.2976-0.0217-0.2215-0.1260.4323-0.15470.06110.2582-0.2510.06250.5616-0.19550.316771.806631.0682-14.4776
61.2603-0.26850.32470.06760.06133.19950.2868-0.5462-0.7517-0.08890.14050.17230.0251-0.5047-0.42730.465-0.1421-0.18960.36240.46970.625938.491-8.8029-26.7431
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 - 417
10X-RAY DIFFRACTION5B77 - 129
11X-RAY DIFFRACTION5B222 - 416
13X-RAY DIFFRACTION6C77 - 129
14X-RAY DIFFRACTION6C222 - 416
9X-RAY DIFFRACTION4A501
12X-RAY DIFFRACTION5B501
15X-RAY DIFFRACTION6C501

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