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- PDB-2a65: Crystal structure of LEUTAA, a bacterial homolog of Na+/Cl--depen... -

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Basic information

Entry
Database: PDB / ID: 2a65
TitleCrystal structure of LEUTAA, a bacterial homolog of Na+/Cl--dependent neurotransmitter transporters
ComponentsNa(+):neurotransmitter symporter (Snf family)
KeywordsTRANSPORT PROTEIN / membrane protein
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / membrane / LEUCINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsYamashita, A. / Singh, S.K. / Kawate, T. / Jin, Y. / Gouaux, E.
CitationJournal: Nature / Year: 2005
Title: Crystal structure of a bacterial homologue of Na(+)/Cl(-)-dependent neurotransmitter transporters.
Authors: Yamashita, A. / Singh, S.K. / Kawate, T. / Jin, Y. / Gouaux, E.
History
DepositionJul 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,75210
Polymers58,0771
Non-polymers1,6749
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Na(+):neurotransmitter symporter (Snf family)
hetero molecules

A: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,50420
Polymers116,1552
Non-polymers3,34918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6880 Å2
ΔGint-62 kcal/mol
Surface area39260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.860, 86.310, 81.020
Angle α, β, γ (deg.)90.00, 95.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 6 molecules A

#1: Protein Na(+):neurotransmitter symporter (Snf family) / LEUTAA


Mass: 58077.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O67854
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 214 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEGMME550, NaCl, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.210.995
SYNCHROTRONALS 8.2.220.9793, 0.9795, 0.9641
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDDec 12, 2004
ADSC QUANTUM 3152CCDDec 12, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal, Si(111)SINGLE WAVELENGTHMx-ray1
2Double crystal, Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9951
20.97931
30.97951
40.96411
ReflectionResolution: 1.65→50 Å / Num. obs: 70306 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 23.5 Å2 / Rsym value: 0.082 / Net I/σ(I): 30.5
Reflection shellResolution: 1.65→1.71 Å / Mean I/σ(I) obs: 1.81 / Num. unique all: 6195 / Rsym value: 0.554 / % possible all: 85.9

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→50 Å / Data cutoff high absF: 1843610 / Data cutoff low absF: 0 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3563 4.9 %RANDOM
Rwork0.199 ---
all-70306 --
obs-70261 97.2 %-
Solvent computationSolvent model: flat model / Bsol: 89.176 Å2 / ksol: 0.443 e/Å3
Displacement parametersBiso mean: 29.213 Å2
Baniso -1Baniso -2Baniso -3
1--2.561 Å20 Å22.901 Å2
2--1.847 Å20 Å2
3---0.714 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 112 210 4366
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.11
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.96
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.2231.5
X-RAY DIFFRACTIONc_mcangle_it1.8912
X-RAY DIFFRACTIONc_scbond_it1.9012
X-RAY DIFFRACTIONc_scangle_it2.9022.5
LS refinement shellResolution: 1.65→1.71 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3199 318 4.4 %
Rwork0.2939 5786 -
obs-6104 84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3BOG_XPLOR_PAR.TXTBOG_XPLOR_TOP.TXT
X-RAY DIFFRACTION4ION.PARAMION.TOP

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