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- PDB-6bmi: Crystal Structure of GltPh R397C in complex with L-Serine -

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Basic information

Entry
Database: PDB / ID: 6bmi
TitleCrystal Structure of GltPh R397C in complex with L-Serine
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
SERINE / Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 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
DepositionNov 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Author supporting evidence / Structure summary / Category: audit_author / pdbx_audit_support
Item: _audit_author.identifier_ORCID / _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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

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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)133,17710
Polymers132,7703
Non-polymers4077
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-114 kcal/mol
Surface area47200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.750, 114.750, 322.336
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.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO3

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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: 4.61 Å3/Da / Density % sol: 73.34 % / 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 15-32% 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: Jul 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.9→47.48 Å / Num. obs: 20718 / % possible obs: 94.9 % / Redundancy: 3.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.063 / Rrim(I) all: 0.088 / Net I/σ(I): 8.5
Reflection shellResolution: 3.9→4.27 Å / Redundancy: 3 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 15254 / CC1/2: 0.722 / Rpim(I) all: 0.778 / % possible all: 95.8

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Processing

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

2nwx


Resolution: 3.9→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.921 / SU ML: 0.494 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.674
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 1025 5 %RANDOM
Rwork0.2268 ---
obs0.2279 19548 94.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 314.02 Å2 / Biso min: 99.71 Å2
Baniso -1Baniso -2Baniso -3
1-4.98 Å22.49 Å2-0 Å2
2--4.98 Å2-0 Å2
3----7.48 Å2
Refinement stepCycle: final / Resolution: 3.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8871 0 22 0 8893
Biso mean--146.69 --
Num. residues----1200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229038
X-RAY DIFFRACTIONr_angle_refined_deg1.061.99512311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.40451195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01324.368261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.624151508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1181521
X-RAY DIFFRACTIONr_chiral_restr0.0720.21568
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216407
Refine LS restraints NCS

Ens-ID: 1 / Number: 2942 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.020.05
2BTIGHT POSITIONAL0.020.05
3CTIGHT POSITIONAL0.020.05
1ATIGHT THERMAL0.030.5
2BTIGHT THERMAL0.020.5
3CTIGHT THERMAL0.020.5
LS refinement shellResolution: 3.9→3.998 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 72 -
Rwork0.326 1434 -
all-1506 -
obs--96.05 %
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)
13.7729-0.314-0.83791.5245-0.17662.85110.2184-0.1093-0.2415-0.2586-0.2117-0.2477-0.2128-0.4271-0.00670.5044-0.09940.02160.28620.06560.06848.7158.924-10.394
23.2275-0.71380.84653.0599-1.07181.2853-0.2353-0.547-0.97130.11760.0597-0.740.72670.52770.17561.16970.50950.15890.77640.22080.87740.958-18.3362.848
31.7199-0.16730.11576.12840.94541.3172-0.0675-0.1330.48730.67660.2353-0.7486-0.47731.1557-0.16780.8072-0.47220.2251.1331-0.06150.82548.53224.8591.099
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 416
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION2B9 - 416
4X-RAY DIFFRACTION2B501 - 502
5X-RAY DIFFRACTION3C9 - 416
6X-RAY DIFFRACTION3C501 - 503

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