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- PDB-6wtx: Structure of VcINDY in complex with terephthalate -

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Basic information

Entry
Database: PDB / ID: 6wtx
TitleStructure of VcINDY in complex with terephthalate
ComponentsDASS family sodium-coupled anion symporter
KeywordsTRANSPORT PROTEIN / Transporter / MEMBRANE PROTEIN
Function / homologySolute carrier family 13 / Sodium/sulphate symporter, conserved site / transmembrane transporter activity / integral component of membrane / Transporter, NadC family
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.92 Å
AuthorsSauer, D.B. / Marden, J.J. / Wang, D.N.
Funding support United States, 3items
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
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
C: DASS family sodium-coupled anion symporter
D: DASS family sodium-coupled anion symporter
A: DASS family sodium-coupled anion symporter
B: DASS family sodium-coupled anion symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,47816
Polymers192,6294
Non-polymers84812
Water0
1
C: DASS family sodium-coupled anion symporter
D: DASS family sodium-coupled anion symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7398
Polymers96,3152
Non-polymers4246
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DASS family sodium-coupled anion symporter
B: DASS family sodium-coupled anion symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7398
Polymers96,3152
Non-polymers4246
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)108.458, 103.062, 174.447
Angle α, β, γ (deg.)90.000, 95.848, 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-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 18 through 462)
d_3ens_1(chain "C" and resid 18 through 462)
d_4ens_1(chain "D" and resid 18 through 462)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUGLNE1 - 445
d_21ens_1LEUGLNF1 - 445
d_31ens_1LEUGLNA1 - 445
d_41ens_1LEUGLNC1 - 445

NCS oper:
IDCodeMatrixVector
1given(0.17881747953, -0.26769583762, -0.946764620978), (-0.263848609377, -0.940074780717, 0.215970641501), (-0.947843985234, 0.211183202886, -0.238732977349)-74.3699631073, -48.9424476476, -78.903405897
2given(-0.967565221173, -0.0128845403398, 0.252292551213), (-0.0135317278167, 0.999908097267, -0.000830278188599), (-0.252258667085, -0.00421730243238, -0.967650649377)-24.1344537603, 22.4611615268, -81.8146948528
3given(-0.408632630453, 0.323667314057, 0.853380831247), (-0.262338623631, -0.937204036619, 0.229841337221), (0.874184088096, -0.129954082487, 0.467882588439)28.4875520169, -25.3625225035, 13.5106053603

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Components

#1: Protein
DASS family sodium-coupled anion symporter / Transporter / NadC family


Mass: 48157.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC0395_0108, GG844_00510 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3AG83
#2: Chemical
ChemComp-UB7 / terephthalic acid / benzene-1,4-dicarboxylic acid / Terephthalic acid


Mass: 166.131 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
Has ligand of interestY

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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: 5.04 Å3/Da / Density % sol: 75.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30% PEG 550, 100mM Tris pH 8.0, 50mM NaCl

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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: Nov 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 33199 / % possible obs: 97.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 7.1 Å2 / Rsym value: 0.112 / Net I/σ(I): 13.3
Reflection shellResolution: 3.9→3.97 Å / Num. unique obs: 1665 / CC1/2: 0.814

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ul9
Resolution: 3.92→47.8 Å / SU ML: 0.5189 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.1207
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3084 2000 6.98 %
Rwork0.2902 26638 -
Obs0.2915 28638 82.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 5.64 Å2
Refinement stepCycle: LAST / Resolution: 3.92→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13372 0 56 0 13428
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005913736
X-RAY DIFFRACTIONf_angle_d1.16618728
X-RAY DIFFRACTIONf_chiral_restr0.06652320
X-RAY DIFFRACTIONf_plane_restr0.01032268
X-RAY DIFFRACTIONf_dihedral_angle_d6.07351824
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefinement-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS0.347817121648
ens_1d_3CX-RAY DIFFRACTIONTorsion NCS0.251664234019
ens_1d_4DX-RAY DIFFRACTIONTorsion NCS0.30342712955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
3.92-4.010.4453820.3531082X-RAY DIFFRACTION46.97
4.01-4.120.33071030.32571390X-RAY DIFFRACTION60.99
4.12-4.240.35751140.31251517X-RAY DIFFRACTION66.41
4.24-4.380.33341240.29931660X-RAY DIFFRACTION72.64
4.38-4.540.29011350.29181788X-RAY DIFFRACTION77.76
4.54-4.720.30331430.28671913X-RAY DIFFRACTION82.64
4.72-4.930.3011510.27592006X-RAY DIFFRACTION87.79
4.93-5.190.30581570.29292099X-RAY DIFFRACTION91.04
5.19-5.520.30341670.30082225X-RAY DIFFRACTION97
5.52-5.940.31511730.31192295X-RAY DIFFRACTION99.52
5.94-6.540.34751720.28542300X-RAY DIFFRACTION99.56
6.54-7.480.2441730.26332303X-RAY DIFFRACTION98.92
7.49-9.420.22541590.21322118X-RAY DIFFRACTION90.75
9.42-47.80.29891470.29231942X-RAY DIFFRACTION81.28

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