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- PDB-6bau: Crystal Structure of GltPh R397C in complex with L-Cysteine -

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Basic information

Entry
Database: PDB / ID: 6bau
TitleCrystal Structure of GltPh R397C in complex with L-Cysteine
ComponentsGlutamate transporter homolog
KeywordsTRANSPORT PROTEIN / Amino acid transporter Transmembrane transporter Aspartate transporter
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
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
CYSTEINE / Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsFont, J. / Scopelliti, A.J. / Vandenberg, R.J. / Boudker, O. / Ryan, R.M.
Funding support Australia, United States, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1048784 Australia
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS064357 United States
CitationJournal: Nat Commun / Year: 2018
Title: Structural characterisation reveals insights into substrate recognition by the glutamine transporter ASCT2/SLC1A5.
Authors: Scopelliti, A.J. / Font, J. / Vandenberg, R.J. / Boudker, O. / Ryan, R.M.
History
DepositionOct 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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: Glutamate transporter homolog
B: Glutamate transporter homolog
C: Glutamate transporter homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,27112
Polymers132,7703
Non-polymers5019
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-104 kcal/mol
Surface area46920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.313, 115.313, 322.274
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
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 Glutamate transporter homolog / Glt(Ph) / Sodium-aspartate symporter Glt(Ph) / Sodium-dependent aspartate transporter


Mass: 44256.660 Da / Num. of mol.: 3 / Mutation: R397C
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: PBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: O59010
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO2S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.81 Å3/Da / Density % sol: 74.43 % / Description: Sword
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM citric acid 50 mM Disodium phosphate 100 mM Lithium sulfate 15-23% PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.8→49.34 Å / Num. obs: 23104 / % possible obs: 96.9 % / Redundancy: 3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.069 / Rrim(I) all: 0.125 / Net I/σ(I): 6.2
Reflection shellResolution: 3.8→4.01 Å / Redundancy: 3 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 10244 / CC1/2: 0.723 / Rpim(I) all: 0.508 / Rrim(I) all: 0.905 / % possible all: 98.4

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NWX

2nwx


Resolution: 3.8→40 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.882 / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2898 1253 5.4 %RANDOM
Rwork0.2668 ---
obs0.268 21793 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 295.37 Å2 / Biso min: 84.55 Å2
Baniso -1Baniso -2Baniso -3
1-5.12 Å22.56 Å2-0 Å2
2--5.12 Å2-0 Å2
3----7.69 Å2
Refinement stepCycle: final / Resolution: 3.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9003 0 27 0 9030
Biso mean--97.63 --
Num. residues----1224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229177
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.99512507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.67751221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61924.368261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.041151518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9051521
X-RAY DIFFRACTIONr_chiral_restr0.0660.21590
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216531
Refine LS restraints NCS

Ens-ID: 1 / Number: 3010 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL00
2BTIGHT POSITIONAL00
3CTIGHT POSITIONAL00
1ATIGHT THERMAL0.150.5
2BTIGHT THERMAL0.080.5
3CTIGHT THERMAL0.10.5
LS refinement shellResolution: 3.8→3.898 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.365 104 -
Rwork-1633 -
obs--98.08 %
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)
10.070.6808-0.0170.27980.23921.1887-0.02420.1992-0.11740.19520.060.2383-0.01610.181-0.03590.76020.12210.01080.6848-0.10190.4033.45-12.789-9.773
20.38680.3648-0.78080.3779-0.75750.42510.28620.0092-0.17440.1196-0.18140.5522-0.1535-0.1616-0.10480.557-0.00860.05161.2728-0.13940.656-36.264-26.8613.52
31.7043-0.81080.04820.1437-0.2942-0.981-0.0159-0.4734-0.1808-0.18250.05750.0210.2814-0.1754-0.04161.15130.1115-0.30560.5497-0.22960.6068-2.454-55.1981.604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 416
2X-RAY DIFFRACTION1A501 - 503
3X-RAY DIFFRACTION2B9 - 416
4X-RAY DIFFRACTION2B501 - 503
5X-RAY DIFFRACTION3C9 - 416
6X-RAY DIFFRACTION3C501 - 503

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