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- PDB-6wtw: Structure of LaINDY crystallized in the presence of alpha-ketoglu... -

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Basic information

Entry
Database: PDB / ID: 6wtw
TitleStructure of LaINDY crystallized in the presence of alpha-ketoglutarate and malate
ComponentsDASS family sodium-coupled anion symporter
KeywordsTRANSPORT PROTEIN / Transporter / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS / MEMBRANE PROTEIN
Function / homologySolute carrier family 13 / Citrate carrier CitT-related / transmembrane transporter activity / integral component of membrane / DASS family sodium-coupled anion symporter
Function and homology information
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsSauer, D.B. / Cocco, N. / Marden, J.J. / Song, J.M. / Wang, D.N. / New York Consortium on Membrane Protein Structure (NYCOMPS)
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS108151 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121994 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK099023 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DASS family sodium-coupled anion symporter
B: DASS family sodium-coupled anion symporter


Theoretical massNumber of molelcules
Total (without water)107,0792
Polymers107,0792
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-59 kcal/mol
Surface area36960 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)91.328, 76.609, 96.946
Angle α, β, γ (deg.)90.000, 90.485, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 0 through 265 or (resid 266...A0 - 487
211chain 'B'B0 - 487

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Components

#1: Protein DASS family sodium-coupled anion symporter


Mass: 53539.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: D7H66_01865 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A9Y7Q2

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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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 30% Jeffamine ED-2001, 100 mM HEPES pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.86→50.09 Å / Num. obs: 30640 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 71.52 Å2 / CC1/2: 0.966 / Net I/σ(I): 16
Reflection shellResolution: 2.86→2.9 Å / Num. unique obs: 1410 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIXdev_3707refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WU1
Resolution: 2.86→50.09 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.6932
RfactorNum. reflection% reflection
Rfree0.2748 2011 6.57 %
Rwork0.2204 --
Obs0.2239 30589 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 73.46 Å2
Refinement stepCycle: LAST / Resolution: 2.86→50.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7504 0 0 0 7504
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00587718
X-RAY DIFFRACTIONf_angle_d0.939510534
X-RAY DIFFRACTIONf_chiral_restr0.05091242
X-RAY DIFFRACTIONf_plane_restr0.00731254
X-RAY DIFFRACTIONf_dihedral_angle_d6.13541016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
2.86-2.930.36611210.30181524X-RAY DIFFRACTION74.7
2.93-3.010.34931450.28082021X-RAY DIFFRACTION97.96
3.01-3.10.34681490.26312038X-RAY DIFFRACTION99.41
3.1-3.20.2841440.24092088X-RAY DIFFRACTION99.82
3.2-3.310.33821280.2412080X-RAY DIFFRACTION99.86
3.31-3.440.28811480.22942061X-RAY DIFFRACTION99.91
3.45-3.60.2871490.22162083X-RAY DIFFRACTION100
3.6-3.790.30171470.21812079X-RAY DIFFRACTION99.96
3.79-4.030.25331500.21482085X-RAY DIFFRACTION99.91
4.03-4.340.25831440.20362064X-RAY DIFFRACTION100
4.34-4.780.26651300.18442129X-RAY DIFFRACTION100
4.78-5.470.2491500.19922079X-RAY DIFFRACTION99.91
5.47-6.880.25411490.24692106X-RAY DIFFRACTION99.96
6.89-50.090.25981570.21772141X-RAY DIFFRACTION99.39
Refinement TLS params.Method: refined / Origin x: -25.6886249193 Å / Origin y: 6.20677519193 Å / Origin z: -24.3539988797 Å
111213212223313233
T0.557159847268 Å20.04080727828 Å20.0424983623239 Å2-0.327313844475 Å2-0.0103285257806 Å2--0.580393361488 Å2
L2.04911468759 °20.685779821006 °2-0.109605286114 °2-0.871780926024 °2-0.096518779062 °2--0.346793023514 °2
S0.102191510102 Å °-0.107628846572 Å °-0.0476691818167 Å °0.22166509773 Å °-0.0764011824466 Å °-0.0794249220596 Å °-0.0325068159649 Å °0.0288044293203 Å °-0.0319878785031 Å °
Refinement TLS groupSelection details: all

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