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- PDB-3tu0: Crystal structure of T355V, S354A, K288A LeuT mutant in complex w... -

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Basic information

Entry
Database: PDB / ID: 3tu0
TitleCrystal structure of T355V, S354A, K288A LeuT mutant in complex with alanine and sodium
ComponentsLeucine transporter LeuT
KeywordsTRANSPORT PROTEIN / LeuT-fold / sodium-dependent amino acid transporter / plasma membrane
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / membrane / ALANINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.994 Å
AuthorsKrishnamurthy, H. / Gouaux, E.
CitationJournal: Nature / Year: 2012
Title: X-ray structures of LeuT in substrate-free outward-open and apo inward-open states.
Authors: Krishnamurthy, H. / Gouaux, E.
History
DepositionSep 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Jan 25, 2012Group: Database references
Revision 1.3Feb 1, 2012Group: Database references
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine transporter LeuT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1133
Polymers58,0011
Non-polymers1122
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Leucine transporter LeuT
hetero molecules

A: Leucine transporter LeuT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2276
Polymers116,0032
Non-polymers2244
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2900 Å2
ΔGint-60 kcal/mol
Surface area36730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.331, 87.346, 81.687
Angle α, β, γ (deg.)90.00, 95.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Leucine transporter LeuT


Mass: 58001.367 Da / Num. of mol.: 1 / Mutation: T354V, S355A, K288A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: snf, aq_2077 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O67854
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 26-28% PEG550 MME, 100 mM HEPES, 200 mM sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Double-crystal Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.946→20 Å / Num. all: 12659 / Num. obs: 12469 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 65.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.3
Reflection shellResolution: 2.946→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.9 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A65

2a65


Resolution: 2.994→19.791 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 28.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2884 671 5.39 %RANDOM
Rwork0.2175 ---
obs0.2213 12457 98.51 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.954 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-27.6922 Å20 Å28.3984 Å2
2---12.329 Å2-0 Å2
3----15.3633 Å2
Refinement stepCycle: LAST / Resolution: 2.994→19.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 7 0 4046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034171
X-RAY DIFFRACTIONf_angle_d0.7365682
X-RAY DIFFRACTIONf_dihedral_angle_d16.2671423
X-RAY DIFFRACTIONf_chiral_restr0.048641
X-RAY DIFFRACTIONf_plane_restr0.003695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.994-3.2240.34441440.28942205X-RAY DIFFRACTION94
3.224-3.54670.32361460.24752364X-RAY DIFFRACTION99
3.5467-4.05610.27471290.21422366X-RAY DIFFRACTION100
4.0561-5.09580.29141240.19132410X-RAY DIFFRACTION100
5.0958-19.79170.25721280.21042441X-RAY DIFFRACTION100

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