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- PDB-6bav: Crystal Structure of GltPh R397C in complex with S-Benzyl-L-Cysteine -

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Basic information

Entry
Database: PDB / ID: 6bav
TitleCrystal Structure of GltPh R397C in complex with S-Benzyl-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
BENZYLCYSTEINE / Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 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 16, 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)133,4739
Polymers132,7703
Non-polymers7036
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-101 kcal/mol
Surface area46790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.659, 114.659, 321.449
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
1112A1 - 700
2112B1 - 700
3112C1 - 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.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-BCS / BENZYLCYSTEINE


Type: L-peptide linking / Mass: 211.281 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13NO2S

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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: 4.74 Å3/Da / Density % sol: 74.03 % / Description: Sword
Crystal growTemperature: 280 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: Sep 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.7→49.07 Å / Num. obs: 24809 / % possible obs: 97.5 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.046 / Rrim(I) all: 0.091 / Net I/σ(I): 8.7
Reflection shellResolution: 3.7→3.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 12538 / CC1/2: 0.833 / Rpim(I) all: 0.335 / Rrim(I) all: 0.653 / % possible all: 98.9

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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: 2NWW

2nww


Resolution: 3.7→40 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.93 / SU B: 93.68 / SU ML: 0.566 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.611 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 1266 5.1 %RANDOM
Rwork0.2466 ---
obs0.2472 23464 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 325.11 Å2 / Biso mean: 184.509 Å2 / Biso min: 120.59 Å2
Baniso -1Baniso -2Baniso -3
1-6.89 Å23.45 Å2-0 Å2
2--6.89 Å2-0 Å2
3----10.34 Å2
Refinement stepCycle: final / Resolution: 3.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8985 0 45 0 9030
Biso mean--163.77 --
Num. residues----1227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229183
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.99812519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.26851224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29124.535258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.066151494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.931518
X-RAY DIFFRACTIONr_chiral_restr0.0680.21590
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216549
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1640TIGHT POSITIONAL0.130.05
2B1640TIGHT POSITIONAL0.110.05
3C1640TIGHT POSITIONAL0.120.05
1A1370MEDIUM POSITIONAL0.20.5
2B1370MEDIUM POSITIONAL0.180.5
3C1370MEDIUM POSITIONAL0.180.5
1A1640TIGHT THERMAL0.120.5
2B1640TIGHT THERMAL0.090.5
3C1640TIGHT THERMAL0.090.5
1A1370MEDIUM THERMAL0.182
2B1370MEDIUM THERMAL0.132
3C1370MEDIUM THERMAL0.122
LS refinement shellResolution: 3.7→3.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 95 -
Rwork0.375 1728 -
all-1823 -
obs--98.81 %
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)
12.3555-1.10580.54944.8899-0.68914.2872-0.1585-0.02560.0961-0.35370.1418-0.0890.56250.10260.01670.2451-0.1001-0.0530.7374-0.0210.0315-11.8572.744-12.394
23.33970.24160.8464.02691.25874.1085-0.3722-0.23461.01980.4260.224-0.4487-1.50860.78240.14821.3196-0.4364-0.28310.6453-0.02090.9113-4.05343.9751.067
34.50511.7983-1.0944.1561-0.1982.47060.0807-0.45640.47730.68770.00910.8819-0.9174-1.4048-0.08980.75090.5177-0.23431.48010.13640.9805-45.20929.235-0.676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 417
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION2B9 - 417
4X-RAY DIFFRACTION2B501 - 502
5X-RAY DIFFRACTION3C9 - 417
6X-RAY DIFFRACTION3C501 - 502

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