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- PDB-6v4k: Structure of TrkH-TrkA in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 6v4k
TitleStructure of TrkH-TrkA in complex with ADP
Components
  • Potassium transporter peripheral membrane component
  • Trk system potassium uptake protein
KeywordsTRANSPORT PROTEIN / ion channel / TrkH / TrkA / nucleotide binding
Function / homology
Function and homology information


potassium ion transmembrane transporter activity / potassium:chloride symporter activity / integral component of membrane / plasma membrane / metal ion binding
TrkA-N domain / Regulator of K+ conductance, C-terminal / TrkA-C domain / Cation transport protein / Regulator of K+ conductance, C-terminal domain superfamily / NAD(P)-binding domain superfamily / Potassium uptake protein TrkA / TrkH potassium transport family / Cation transporter / Regulator of K+ conductance, N-terminal
Potassium transporter peripheral membrane component / Trk system potassium uptake protein
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53004144504 Å
AuthorsZhou, M. / Zhang, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086392 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK122784 United States
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trk system potassium uptake protein
B: Trk system potassium uptake protein
C: Trk system potassium uptake protein
D: Trk system potassium uptake protein
E: Potassium transporter peripheral membrane component
F: Potassium transporter peripheral membrane component
G: Potassium transporter peripheral membrane component
H: Potassium transporter peripheral membrane component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)414,89912
Polymers413,1908
Non-polymers1,7094
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24520 Å2
ΔGint-127 kcal/mol
Surface area150100 Å2
Unit cell
γ
α
β
Length a, b, c (Å)262.101, 188.495, 187.911
Angle α, β, γ (deg.)90.000, 133.163, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Trk system potassium uptake protein / TrkH


Mass: 53104.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria)
Gene: ACS91_07345, BA740_20060, BS585_02545, C1S91_23870, C9I78_16125, CA163_10465, CGH73_23020, CGJ02_21120, FHP20_22005, WR32_21470
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D1QU68
#2: Protein
Potassium transporter peripheral membrane component / Trk system potassium transport protein TrkA / Trk system potassium transporter TrkA


Mass: 50193.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria)
Gene: trkA, sapG, ACS91_07035, BA740_20405, C1S91_23530, CGH73_23350, CGJ02_20785, WR32_21780
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A072LGS4
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestN

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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: 4.1 Å3/Da / Density % sol: 69.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 100 mM HEPES, pH 7.2, 26% PEG400, 10% 2-propanol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 30, 2017
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 81759 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.3655473934 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 30.63
Reflection shellResolution: 3.52→3.58 Å / Rmerge(I) obs: 1.7 / Num. unique obs: 4081

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4J9U
Resolution: 3.53004144504→49.8219581438 Å / SU ML: 0.370948467346 / Cross valid method: FREE R-VALUE / σ(F): 1.33788131981 / Phase error: 27.9833370918
RfactorNum. reflection% reflection
Rfree0.291089168135 3403 4.93932884347 %
Rwork0.250161637564 --
Obs0.252157814466 68896 84.3104861901 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 80.3680566079 Å2
Refinement stepCycle: LAST / Resolution: 3.53004144504→49.8219581438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28126 0 108 0 28234
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045422674995928844
X-RAY DIFFRACTIONf_angle_d1.0087535857439261
X-RAY DIFFRACTIONf_chiral_restr0.09904376370984646
X-RAY DIFFRACTIONf_plane_restr0.007480485454834955
X-RAY DIFFRACTIONf_dihedral_angle_d20.137992328510171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
3.54-3.58050.375989872566100.315155377211242X-RAY DIFFRACTION7.43801652893
3.5805-3.63390.399256650723420.308007471372811X-RAY DIFFRACTION25.0882352941
3.6339-3.69070.359500958597850.2854664023251214X-RAY DIFFRACTION38.2847038019
3.6907-3.75110.331163866885690.2739685259921646X-RAY DIFFRACTION50.3967087864
3.7511-3.81580.263462208414910.2825278221291905X-RAY DIFFRACTION59.5110316041
3.8158-3.88520.2781093948811270.2820802542662344X-RAY DIFFRACTION73.1497927768
3.8852-3.95990.3330976335711360.2724561267222791X-RAY DIFFRACTION85.5597778427
3.9599-4.04060.3152667660791490.2577372296113045X-RAY DIFFRACTION94.3017419545
4.0406-4.12850.3150650435761440.2558857561793192X-RAY DIFFRACTION98.7859046491
4.1285-4.22450.2764583413821290.2351544936573276X-RAY DIFFRACTION99.7656021096
4.2245-4.330.2996451249851780.2340742547153192X-RAY DIFFRACTION99.8222748815
4.33-4.4470.2893713365391920.2178376193493219X-RAY DIFFRACTION99.8536299766
4.447-4.57780.2548902115091620.2102158352913229X-RAY DIFFRACTION99.7059688327
4.5778-4.72550.256492216871320.2069982088983249X-RAY DIFFRACTION99.4119376654
4.7255-4.89420.2356660423821740.2105783649463196X-RAY DIFFRACTION98.6245244366
4.8942-5.090.2174786999421520.219446711883150X-RAY DIFFRACTION97.6345357776
5.09-5.32140.2742907068331580.2392406382813244X-RAY DIFFRACTION99.8825601879
5.3214-5.60160.3029419521962100.2618783121833191X-RAY DIFFRACTION99.8825256975
5.6016-5.9520.3131487282031940.2957409897763228X-RAY DIFFRACTION99.795858851
5.952-6.41070.3072613839712040.292878115743190X-RAY DIFFRACTION99.5892018779
6.4107-7.05420.3567490069771750.278003971723210X-RAY DIFFRACTION99.5295501323
7.0542-8.07130.3230721962511810.2619954294373199X-RAY DIFFRACTION98.3415769566

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