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- PDB-4dz1: Crystal structure of DalS, an ATP binding cassette transporter fo... -

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Basic information

Entry
Database: PDB / ID: 4dz1
TitleCrystal structure of DalS, an ATP binding cassette transporter for D-alanine from Salmonella enterica
ComponentsDalS D-Alanine transporter
KeywordsTRANSPORT PROTEIN / D-alanine binding / periplasmic
Function / homologyPeriplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / D-ALANINE / :
Function and homology information
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMok, M. / Junop, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Characterization of DalS, an ATP-binding Cassette Transporter for D-Alanine, and Its Role in Pathogenesis in Salmonella enterica.
Authors: Osborne, S.E. / Tuinema, B.R. / Mok, M.C. / Lau, P.S. / Bui, N.K. / Tomljenovic-Berube, A.M. / Vollmer, W. / Zhang, K. / Junop, M. / Coombes, B.K.
History
DepositionFeb 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: DalS D-Alanine transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8592
Polymers29,7701
Non-polymers891
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.076, 81.076, 187.926
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-433-

HOH

21A-436-

HOH

31A-503-

HOH

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Components

#1: Protein DalS D-Alanine transporter / Extracellular solute-binding protein family 3


Mass: 29769.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: LTSEBAI_2502 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: G9W5C4
#2: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 10% w/v PEG3000, 0.1 M sodium/potassium phosphate, pH 6.2, 5 mM glycine, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2011
Details: vertically focusing mirror, horizontally focusing monochromator
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 28940 / Num. obs: 28940 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 21 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 25
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 21 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2761 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→39.047 Å / SU ML: 0.21 / σ(F): 0.3 / Phase error: 18.22 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 2000 6.91 %RANDOM
Rwork0.1898 ---
all0.1908 28940 --
obs0.1907 28934 97.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.779 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.6666 Å20 Å2-0 Å2
2--3.6666 Å2-0 Å2
3----7.2063 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 6 168 1985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121865
X-RAY DIFFRACTIONf_angle_d0.9492517
X-RAY DIFFRACTIONf_dihedral_angle_d12.648690
X-RAY DIFFRACTIONf_chiral_restr0.077272
X-RAY DIFFRACTIONf_plane_restr0.004319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94720.26511360.22871825X-RAY DIFFRACTION95
1.9472-1.99980.24861350.20531819X-RAY DIFFRACTION94
1.9998-2.05870.22131360.18941846X-RAY DIFFRACTION96
2.0587-2.12510.24951400.18651873X-RAY DIFFRACTION97
2.1251-2.20110.21611370.18481862X-RAY DIFFRACTION96
2.2011-2.28920.22881410.17241890X-RAY DIFFRACTION98
2.2892-2.39330.20361420.18481898X-RAY DIFFRACTION97
2.3933-2.51950.2171420.19611920X-RAY DIFFRACTION98
2.5195-2.67730.21731410.18821903X-RAY DIFFRACTION98
2.6773-2.8840.20431450.20891955X-RAY DIFFRACTION98
2.884-3.17410.20931450.20121951X-RAY DIFFRACTION99
3.1741-3.63310.21271480.20091995X-RAY DIFFRACTION100
3.6331-4.57620.16341520.16052042X-RAY DIFFRACTION100
4.5762-39.05490.19511600.1982155X-RAY DIFFRACTION98

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