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- PDB-4us3: Crystal Structure of the bacterial NSS member MhsT in an Occluded... -

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Basic information

Entry
Database: PDB / ID: 4us3
TitleCrystal Structure of the bacterial NSS member MhsT in an Occluded Inward-Facing State
ComponentsTRANSPORTER
KeywordsTRANSPORT PROTEIN / NEUROTRANSMITTER / NEUROTRANSMITTER SODIUM SYMPORTER FAMILY / LEUT FOLD / AMINO ACID TRANSPORTER / SECONDARY TRANSPORTER / MEMBRANE PROTEIN
Function / homology: / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / membrane / TRYPTOPHAN / Sodium-dependent transporter
Function and homology information
Biological speciesBACILLUS HALODURANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsMalinauskaite, L. / Quick, M. / Reinhard, L. / Lyons, J.A. / Yano, H. / Javitch, J.A. / Nissen, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: A Mechanism for Intracellular Release of Na+ by Neurotransmitter/Sodium Symporters
Authors: Malinauskaite, L. / Quick, M. / Reinhard, L. / Lyons, J.A. / Yano, H. / Javitch, J.A. / Nissen, P.
History
DepositionJul 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Nov 19, 2014Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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_database_status.status_code_sf / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: TRANSPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,90014
Polymers48,3611
Non-polymers4,53913
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.280, 49.890, 110.050
Angle α, β, γ (deg.)90.00, 96.76, 90.00
Int Tables number3
Space group name H-MP121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TRANSPORTER / MULTI-HYDROPHOBIC AMINO ACID TRANSPORTER


Mass: 48360.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS HALODURANS (bacteria) / Strain: C-125 / Plasmid: PNZ8048
Production host: LACTOCOCCUS LACTIS SUBSP. CREMORIS NZ9000 (lactic acid bacteria)
References: UniProt: Q9KDT3

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Sugars , 2 types, 10 molecules

#4: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 3 types, 80 molecules

#2: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE LEADING THREE RESIDUES ARE LEFTOVER FROM THE EXPRESSION CONSTRUCT WITH THE LEAD METHIONINE ...THE LEADING THREE RESIDUES ARE LEFTOVER FROM THE EXPRESSION CONSTRUCT WITH THE LEAD METHIONINE REMOVED. NUMBERING IN THE PDB FILE REFLECTS THE UNIPROT SEQUENCE AND NUMBERING

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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: 2.5 Å3/Da / Density % sol: 50.8 %
Description: THE SEARCH MODEL FOR MR_ROSETTA WAS PREPARED WITH PHENIX SCULPTOR USING LEUT PDB ENTRY 2A65 AND PAIRWISE ALIGNMENT WITH MHST SEQUENCE
Crystal growpH: 7
Details: CRYSTALLISED USING HILIDE WITH DOPC AS ADDED LIPID. CRYSTALS WERE OBTAINED IN 20-24% W/W PEG400, 400 MM NACL, 100 MM TRIS-HCL PH 7.0, 5% TRIMETHYLAMINE-N-OXIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 1, 2012 / Details: MIRRORS FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: HORIZONTALLY SIDE DIFFRACTING SI(111) CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.1→44 Å / Num. obs: 27894 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 1.15 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXMR_ROSETTAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PHENIX SCULPTOR MODEL WITH PDB ENTRY 2A65

2a65


Resolution: 2.098→43.972 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 23.94 / Stereochemistry target values: ML
Details: RESIDUES 8-448 BUILT IN THE STRUCTURE. MET A 180 MODELLED WITH AN ALTERNATIVE SIDE CHAIN CONFORMATION
RfactorNum. reflection% reflection
Rfree0.2342 985 3.5 %
Rwork0.1906 --
obs0.1921 27836 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.4 Å2
Refinement stepCycle: LAST / Resolution: 2.098→43.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 201 77 3593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123619
X-RAY DIFFRACTIONf_angle_d1.2394899
X-RAY DIFFRACTIONf_dihedral_angle_d14.8831246
X-RAY DIFFRACTIONf_chiral_restr0.076572
X-RAY DIFFRACTIONf_plane_restr0.006570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.098-2.20860.30891400.2663733X-RAY DIFFRACTION97
2.2086-2.34690.34121150.27013791X-RAY DIFFRACTION98
2.3469-2.52810.25041390.21073820X-RAY DIFFRACTION99
2.5281-2.78250.24921580.19073841X-RAY DIFFRACTION99
2.7825-3.18510.26591450.17973844X-RAY DIFFRACTION99
3.1851-4.01240.19791420.16353861X-RAY DIFFRACTION99
4.0124-43.98170.19631460.17583961X-RAY DIFFRACTION99

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